Reviewed, UniProtKB/Swiss-Prot P04585 (POL_HV1H2)

Names and origin

Protein names

Recommended name:
    Gag-Pol polyprotein
Alternative name(s):
    Pr160Gag-Pol
Cleaved into the following 11 chains:
    1- Recommended name:
            Matrix protein p17
                Short name=MA
    2- Recommended name:
            Capsid protein p24
                Short name=CA
    3- Recommended name:
            Spacer peptide p2
    4- Recommended name:
            Nucleocapsid protein p7
                Short name=NC
    5- Recommended name:
            Transframe peptide
                Short name=TF
    6- Recommended name:
            p6-pol
                Short name=p6*
    7- Recommended name:
            Protease
              EC=3.4.23.16
        Alternative name(s):
            Retropepsin
            PR
    8- Recommended name:
            Reverse transcriptase/ribonuclease H
              EC=2.7.7.49
              EC=2.7.7.7
              EC=3.1.26.4
        Alternative name(s):
            p66 RT
    9- Recommended name:
            p51 RT
    10- Recommended name:
            p15
    11- Recommended name:
            Integrase
                Short name=IN

Gene names

Name:

gag-pol

Organism

Human immunodeficiency virus type 1 (isolate HXB2 group M subtype B) (HIV-1)

Taxonomic identifier

11706 [NCBI]

Taxonomic lineage

Viruses › Retro-transcribing viruses › Retroviridae › Orthoretrovirinae › Lentivirus › Primate lentivirus group

Virus host

Homo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length	1435 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation. Ref.8 Ref.20 Ref.22 Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to plays a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu. Ref.8 Ref.20 Ref.22 Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is dissassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Ref.8 Ref.20 Ref.22 Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity. Ref.8 Ref.20 Ref.22 The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles By similarity. Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends. Ref.8 Ref.20 Ref.22 Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allow the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration. Ref.8 Ref.20 Ref.22
Catalytic activity	Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro. Endonucleolytic cleavage to 5'-phosphomonoester. Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
Cofactor	Binds 2 magnesium ions for reverse transcriptase polymerase activity By similarity. Binds 2 magnesium ions for ribonuclease H (RNase H) activity. Substrate-binding is a precondition for magnesium binding By similarity. Magnesium ions for integrase activity. Binds at least 1, maybe 2 magnesium ions By similarity.
Enzyme regulation	The viral protease is inhibited by many synthetic protease inhibitors (PIs), such as amprenavir, atazanavir, indinavir, loprinavir, nelfinavir, ritonavir and saquinavir. RT can be inhibited either by nucleoside RT inhibitors (NRTIs) or by non nucleoside RT inhibitors (NNRTIs). NRTIs act as chain terminators, whereas NNRTIs inhibit DNA polymerization by binding a small hydrophobic pocket near the RT active site and inducing an allosteric change in this region. Classical NRTIs are abacavir, adefovir (PMEA), didanosine (ddI), lamivudine (3TC), stavudine (d4T), tenofovir (PMPA), zalcitabine (ddC), and zidovudine (AZT). Classical NNRTIs are atevirdine (BHAP U-87201E), delavirdine, efavirenz (DMP-266), emivirine (I-EBU), and nevirapine (BI-RG-587). The tritherapies used as a basic effective treatment of AIDS associate two NRTIs and one NNRTI. Use of protease inhibitors in tritherapy regimens permit more ambitious therapeutic strategies.
Subunit structure	Pre-integration complex interacts with human HMGA1. Matrix protein p17 is a trimer. Interacts with gp120 and human BAF. Capsid is a homodimer. Interacts with human PPIA/CYPA. The protease is a homodimer, whose active site consists of two apposed aspartic acid residues. The reverse transcriptase is a heterodimer of p66 RT and p51 RT (RT p66/p51). Heterodimerization of RT is essential for DNA polymerase activity. Despite the sequence identities, p66 RT and p51 RT have distinct folding. Integrase is a homodimer and possibly can form homotetramer. Integrase interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1. Ref.6 Ref.7 Ref.14 Ref.17
Subcellular location	Matrix protein p17: Virion Potential. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane; Lipid-anchor Potential. Note: Following virus entry, the nuclear localization signal (NLS) of the matrix protein participates with Vpr to the nuclear localization of the viral genome. During virus production, the nuclear export activity of the matrix protein counteracts the NLS to maintain the Gag and Gag-Pol polyproteins in the cytoplasm, thereby directing unspliced RNA to the plasma membrane By similarity. Capsid protein p24: Virion Potential. Nucleocapsid protein p7: Virion Potential. Reverse transcriptase/ribonuclease H: Virion Potential. Integrase: Virion Potential. Host nucleus Potential. Host cytoplasm Potential. Note: Nuclear at initial phase, cytoplasmic at assembly Potential.
Domain	The reverse transcriptase/ribonuclease H (RT) is structured in five subdomains: finger, palm, thumb, connection and RNase H. Within the palm subdomain, the 'primer grip' region is thought to be involved in the positioning of the primer terminus for accomodating the incoming nucleotide. The RNase H domain stabilizes the association of RT with primer-template By similarity. The tryptophan repeat motif is involved in RT p66/p51 dimerization. Integrase core domain contains the D-x(n)-D-x(35)-E motif, named for the phylogenetically conserved glutamic acid and aspartic acid residues and the invariant 35 amino acid spacing between the second and third acidic residues. Each acidic residue of the D,D(35)E motif is independently essential for the 3'-processing and strand transfer activities of purified integrase protein.
Post-translational modification	Specific enzymatic cleavages by the viral protease yield mature proteins. The protease is released by autocatalytic cleavage. The polyprotein is cleaved during and after budding, this process is termed maturation. Proteolytic cleavage of p66 RT removes the RNase H domain to yield the p51 RT subunit. Nucleocapsid protein p7 might be further cleaved after virus entry. Ref.11 Ref.16 Ref.19 Capsid protein p24 is phosphorylated. Matrix protein p17 is tyrosine phosphorylated presumably in the virion by a host kinase. This modification targets the matrix protein to the nucleus.
Miscellaneous	Capsid protein p24 is able to bind macaque TRIM5-alpha or owl monkey TRIMCyp, preventing reverse transcription of the viral genome and succesfull infection of macaque or owl monkey by HIV-1. The reverse transcriptase is an error-prone enzyme that lacks a proof-reading function. High mutations rate is a direct consequence of this characteristic. RT also displays frequent template switching leading to high recombination rate. Recombination mostly occurs between homologous regions of the two copackaged RNA genomes. If these two RNA molecules derive from different viral strains, reverse transcription will give rise to highly recombinated proviral DNAs. HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K). Resistance to inhibitors associated with mutations are observed both in viral protease and in reverse transcriptase. Most of the time, single mutations confer only a modest reduction in drug susceptibility. Combination of several mutations is usually required to develop a high-level drug resistance. These mutations are predominantly found in clade B viruses and not in other genotypes. They are listed in this entry which is a representative of clade B.
Sequence similarities	Contains 2 CCHC-type zinc fingers. Contains 1 integrase catalytic domain. Contains 1 integrase-type DNA-binding domain. Contains 1 integrase-type zinc finger. Contains 1 peptidase A2 domain. Contains 1 reverse transcriptase domain. Contains 1 RNase H domain.

Ontologies

Keywords
Biological process	Capsid maturation DNA integration DNA recombination Host-virus interaction
Cellular component	Capsid protein Cell membrane Cytoplasm Membrane Nucleus Virion
Coding sequence diversity	Ribosomal frameshifting
Disease	AIDS
Domain	Repeat Zinc-finger
Ligand	Magnesium Metal-binding RNA-binding Viral nucleoprotein Zinc
Molecular function	Aspartyl protease DNA-directed DNA polymerase Endonuclease Hydrolase Nuclease Nucleotidyltransferase Protease RNA-directed DNA polymerase Transferase
PTM	Lipoprotein Myristate Phosphoprotein
Technical term	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Biological process	RNA-dependent DNA replication Inferred from electronic annotation. Source: InterPro initiation of viral infection Inferred from Experiment. Source: Reactome interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW proteolysis Inferred from electronic annotation. Source: InterPro provirus integration Inferred from Experiment. Source: Reactome transposition Inferred from electronic annotation. Source: UniProtKB-KW viral procapsid maturation Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytosol Inferred from Experiment. Source: Reactome host cell cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell host cell plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-KW viral capsid Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro DNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA-directed DNA polymerase activity Inferred from electronic annotation. Source: UniProtKB-KW aspartic-type endopeptidase activity Inferred from electronic annotation. Source: UniProtKB-KW integrase activity Inferred from electronic annotation. Source: InterPro magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW ribonuclease H activity Inferred from electronic annotation. Source: EC structural molecule activity Inferred from electronic annotation. Source: UniProtKB-KW zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by ribosomal frameshifting. [Align] [Select]

Note: Translation results in the formation of the Gag polyprotein most of the time. Ribosomal frameshifting at the gag-pol genes boundary occurs at low frequency and produces the Gag-Pol polyprotein. This strategy of translation probably allows the virus to modulate the quantity of each viral protein. Maintenance of a correct Gag to Gag-Pol ratio is essential for RNA dimerization and viral infectivity.

Isoform Gag-Pol polyprotein (identifier: P04585-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Note: Produced by -1 ribosomal frameshifting.

Isoform Gag polyprotein (identifier: P04591-1)

The sequence of this isoform can be found in the external entry P04591-1.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

Note: Produced by conventional translation.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed; by host By similarity

Chain

2 – 1435

1434

Gag-Pol polyprotein

PRO_0000223620

Chain

2 – 132

131

Matrix protein p17 By similarity

PRO_0000042439

Chain

133 – 363

231

Capsid protein p24 By similarity

PRO_0000042440

Peptide

364 – 377

14

Spacer peptide p2 By similarity

PRO_0000042441

Chain

378 – 432

55

Nucleocapsid protein p7 By similarity

PRO_0000042442

Peptide

433 – 440

8

Transframe peptide Potential

PRO_0000246716

Chain

441 – 488

48

p6-pol Potential

PRO_0000042443

Chain

489 – 587

99

Protease

PRO_0000038665

Chain

588 – 1147

560

Reverse transcriptase/ribonuclease H

PRO_0000042444

Chain

588 – 1027

440

p51 RT

PRO_0000042445

Chain

1028 – 1147

120

p15

PRO_0000042446

Chain

1148 – 1435

288

Integrase By similarity

PRO_0000042447

Regions

Domain

508 – 577

70

Peptidase A2

Domain

631 – 821

191

Reverse transcriptase

Domain

1021 – 1144

124

RNase H

Domain

1201 – 1351

151

Integrase catalytic

Zinc finger

390 – 407

18

CCHC-type 1

Zinc finger

411 – 428

18

CCHC-type 2

Zinc finger

1150 – 1191

42

Integrase-type

DNA binding

1370 – 1417

48

Integrase-type

Region

217 – 225

9

PPIA/CYPA-binding loop

Region

814 – 822

9

RT 'primer grip' By similarity

Motif

16 – 22

7

Nuclear export signal By similarity

Motif

26 – 32

7

Nuclear localization signal By similarity

Motif

985 – 1001

17

Tryptophan repeat motif By similarity

Sites

Active site

513

1

For protease activity; shared with dimeric partner By similarity

Metal binding

697

1

Magnesium; catalytic; for reverse transcriptase activity By similarity

Metal binding

772

1

Magnesium; catalytic; for reverse transcriptase activity By similarity

Metal binding

773

1

Magnesium; catalytic; for reverse transcriptase activity By similarity

Metal binding

1030

1

Magnesium; catalytic; for RNase H activity

Metal binding

1065

1

Magnesium; catalytic; for RNase H activity

Metal binding

1085

1

Magnesium; catalytic; for RNase H activity

Metal binding

1136

1

Magnesium; catalytic; for RNase H activity

Metal binding

1211

1

Magnesium; catalytic; for integrase activity By similarity

Metal binding

1263

1

Magnesium; catalytic; for integrase activity By similarity

Site

132 – 133

2

Cleavage; by viral protease By similarity

Site

221 – 222

2

Cis/trans isomerization of proline peptide bond; by human PPIA/CYPA

Site

363 – 364

2

Cleavage; by viral protease By similarity

Site

377 – 378

2

Cleavage; by viral protease By similarity

Site

393 – 394

2

Cleavage; by viral protease Potential

Site

426 – 427

2

Cleavage; by viral protease Potential

Site

432 – 433

2

Cleavage; by viral protease Potential

Site

440 – 441

2

Cleavage; by viral protease By similarity

Site

488 – 489

2

Cleavage; by viral protease By similarity

Site

587 – 588

2

Cleavage; by viral protease By similarity

Site

988

1

Essential for RT p66/p51 heterodimerization By similarity

Site

1001

1

Essential for RT p66/p51 heterodimerization By similarity

Site

1027 – 1028

2

Cleavage; by viral protease; partial By similarity

Site

1147 – 1148

2

Cleavage; by viral protease By similarity

Amino acid modifications

Modified residue

132

1

Phosphotyrosine; by host By similarity

Lipidation

2

1

N-myristoyl glycine; by host By similarity

Natural variations

Natural variant

496

1

R → K Confers to resistance to A-77003; when associated with other amino acid changes.

Natural variant

496

1

R → Q Confers to resistance to A-77003.

Natural variant

498

1

L → F Confers resistance to amprenavir, atazanavir, lopinavir; when associated with other amino acid changes.

Natural variant

498

1

L → I Confers resistance to indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

498

1

L → R Confers resistance to indinavir and lopinavir; when associated with other amino acid changes.

Natural variant

498

1

L → V Confers resistance to indinavir and lopinavir; when associated with other amino acid changes.

Natural variant

498

1

L → Y Confers resistance to atazanavir; when associated with other amino acid changes.

Natural variant

503

1

I → V Confers resistance to tipranavir.

Natural variant

504

1

G → E Confers resistance to lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

508

1

K → I Confers resistance to lopinavir.

Natural variant

508

1

K → M Confers resistance to indinavir, lopinavir and nelfinavir; when associated with other amino acid changes.

Natural variant

508

1

K → R Confers resistance to indinavir, lopinavir and ritonavir; when associated with other amino acid changes.

Natural variant

511

1

L → I Confers resistance to BILA 2185 BS.

Natural variant

512

1

L → I Confers resistance to amprenavir, indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

518

1

D → N Confers resistance to nelfinavir; when associated with other amino acid changes.

Natural variant

520

1

V → I Confers resistance to A-77003, amprenavir, atazanavir, indinavir, kynostatin, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

521

1

L → F Confers resistance to atazanavir nelfinavir and ritonavir; when associated with other amino acid changes.

Natural variant

522

1

E → Q Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

523

1

E → D Confers resistance to tipranavir.

Natural variant

524

1

M → I Confers resistance to nelfinavir and ritonavir; when associated with other amino acid changes.

Natural variant

524

1

M → L Confers resistance to ritonavir; when associated with other amino acid changes.

Natural variant

525

1

S → D Confers resistance to indinavir and tipranavir; when associated with other amino acid changes.

Natural variant

529

1

R → K Confers resistance to tipranavir.

Natural variant

533

1

K → I Confers resistance to DMD-323; when associated with other amino acid changes.

Natural variant

534

1

M → F Confers resistance to A-77003.

Natural variant

534

1

M → I Confers resistance to A-77003, amprenavir, atazanavir, indinavir, kynostatin, lopinavir, ritonavir, saquinavir and telinavir; when associated with other amino acid changes.

Natural variant

534

1

M → L Confers resistance to A-77003, amprenavir, indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

535

1

I → V Confers resistance to amprenavir, lopinavir, kynostatin, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

536

1

G → V Confers resistance to A-77003, amprenavir, indinavir, ritonavir, saquinavir and telinavir; when associated with other amino acid changes.

Natural variant

538

1

I → L Confers resistance to atazanavir; when associated with other amino acid changes.

Natural variant

538

1

I → V Confers resistance to amprenavir, lopinavir and ritonavir; when associated with other amino acid changes.

Natural variant

541

1

F → L Confers resistance to lopinavir and telinavir; when associated with other amino acid changes.

Natural variant

541

1

F → Y Confers resistance to indinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

542

1

I → A Confers resistance to lopinavir.

Natural variant

542

1

I → L Confers resistance to amprenavir and lopinavir; when associated with other amino acid changes.

Natural variant

542

1

I → M Confers resistance to amprenavir and lopinavir.

Natural variant

542

1

I → S Confers resistance to lopinavir.

Natural variant

542

1

I → T Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

542

1

I → V Confers resistance to indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

543

1

K → R Confers resistance to nelfinavir.

Natural variant

545

1

R → K Confers resistance to nelfinavir.

Natural variant

546

1

Q → E Confers resistance to lopinavir and ritonavir; when associated with other amino acid changes.

Natural variant

548

1

D → E Confers resistance to tripanavir.

Natural variant

549

1

Q → H Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

551

1

L → P Confers resistance to atazanavir, indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

551

1

L → T Confers resistance to lopinavir.

Natural variant

553

1

E → Q Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

554

1

I → F Confers resistance to indinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

557

1

H → Y Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

559

1

A → I Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

559

1

A → L Confers resistance to lopinavir; when associated with other amino acid changes.

Natural variant

559

1

A → T Confers resistance to A-77003, indinavir, lopinavir, nelfinavir and tripanavir; when associated with other amino acid changes.

Natural variant

559

1

A → V Confers resistance to amprenavir, atazanavir, indinavir, kynostatin, lopinavir, nelfinavir, ritonavir, saquinavir and telinavir; when associated with other amino acid changes.

Natural variant

561

1

G → S Confers resistance to indinavir, nelfinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

565

1

V → I Confers resistance to indinavir, nelfinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

570

1

V → A Confers resistance to A-77003, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

570

1

V → F Confers resistance to lopinavir and ritonavir; when associated with other amino acid changes.

Natural variant

570

1

V → I Confers resistance to A-77003 and kynostatin; when associated with other amino acid changes.

Natural variant

570

1

V → S Confers resistance to lopinavir and ritonavir.

Natural variant

570

1

V → T Confers resistance to indinavir, lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

572

1

I → A Confers resistance to atazanavir, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

572

1

I → V Confers resistance to amprenavir, atazanavir, indinavir, kynostatin, lopinavir, nelfinavir, ritonavir, saquinavir and telinavir; when associated with other amino acid changes.

Natural variant

576

1

N → D Confers resistance to nelfinavir; when associated with other amino acid changes.

Natural variant

576

1

N → S Confers resistance to atazanavir, indinavir and nelfinavir; when associated with other amino acid changes.

Natural variant

577

1

L → M Confers resistance to atazanavir; when associated with other amino acid changes.

Natural variant

578

1

L → M Confers resistance to indinavir, lopinavir, nelfinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

579

1

T → S Confers resistance to lopinavir, ritonavir and saquinavir; when associated with other amino acid changes.

Natural variant

581

1

I → L Confers resistance to indinavir.

Natural variant

628

1

M → L Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

631

1

E → A Confers resistance to lamivudine.

Natural variant

631

1

E → D Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

639

1

P → R Confers resistance to stavudine.

Natural variant

641

1

N → D Confers resistance to stavudine.

Natural variant

649

1

A → V Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

652

1

K → R Confers resistance to abacavir, adefovir, didenosine, lamivudine, stavudine, tenofir and zidovuline; when associated with other amino acid changes.

Natural variant

654

1

D → A Confers resistance to zidovudine.

Natural variant

654

1

D → E Confers multi-NRTI resistance.

Natural variant

654

1

D → G Confers multi-NRTI resistance.

Natural variant

654

1

D → N Confers resistance to zidovudine.

Natural variant

654

1

D → S Confers multi-NRTI resistance.

Natural variant

655

1

S → G Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

655

1

S → N Confers multi-NRTI resistance.

Natural variant

655

1

S → Y Confers multi-NRTI resistance.

Natural variant

656

1

T → A Confers resistance to lamivudine and stavudine.

Natural variant

656

1

T → D Confers resistance to lamivudine, stavudine and rarely to zalcitabine.

Natural variant

656

1

T → G Confers resistance to didanosine, zalcitabine and zidovudine.

Natural variant

656

1

T → N Confers resistance to lamivudine and stavudine.

Natural variant

657

1

K → E Confers resistance to adefovir and lamivudine.

Natural variant

657

1

K → R Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

657

1

K → S Confers resistance to didanosine and stavudine.

Natural variant

661

1

L → I Confers resistance to HBY 097.

Natural variant

661

1

L → V Confers resistance to abacavir, didanosine, HBY 097 and zalcitabine; when associated with other amino acid changes.

Natural variant

662

1

V → I Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

662

1

V → L Confers resistance to HBY 097.

Natural variant

662

1

V → M Confers resistance to stavudine and zalcitabine.

Natural variant

662

1

V → T Confers resistance to d4C, didanosine, stavudine and zalcitabine.

Natural variant

664

1

F → L Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

675

1

W → G Confers resistance to pyrophosphate analog PFA.

Natural variant

675

1

W → S Confers resistance to pyrophosphate analog PFA.

Natural variant

676

1

E → G Confers resistance to pyrophosphate analog PFA.

Natural variant

676

1

E → K Confers resistance to pyrophosphate analog PFA.

Natural variant

679

1

L → I Confers resistance to pyrophosphate analog PFA.

Natural variant

687

1

L → I Confers resistance to nevirapine and efavirenz.

Natural variant

688

1

K → E Confers resistance to atevirdine, efavirenz, nevirapine and zidovudine.

Natural variant

688

1

K → P Confers resistance to TMC125; when associated with E-142.

Natural variant

688

1

K → Q Confers resistance to efavirenz; when associated with I-19.

Natural variant

690

1

K → E Confers resistance to atevirdine; when associated with other amino acid changes.

Natural variant

690

1

K → N Confers resistance to atevirdine, efavirenz, emivirine and nevirapine; when associated with other amino acid changes.

Natural variant

690

1

K → R Confers resistance to emivirine and trovirdine; when associated with other D-179 and C-181.

Natural variant

693

1

V → A Confers resistance to nevirapine.

Natural variant

693

1

V → I Confers resistance to HBY 097.

Natural variant

693

1

V → M Confers resistance to delavirdine, efavirenz and nevirapine.

Natural variant

695

1

V → I Confers resistance to efavirenz, emivirine, nevirapine and trovirdine; when associated with other amino acid changes.

Natural variant

702

1

Y → F Confers resistance to abacavir; when associated with other amino acid changes.

Natural variant

703

1

F → Y Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

705

1

V → I Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

706

1

P → S Confers resistance to lodenosine.

Natural variant

722

1

I → L Confers resistance to delavirdine, efavirenz and nevirapine; when associated with I-239.

Natural variant

722

1

I → M Confers resistance to delavirdine, efavirenz and nevirapine; when associated with I-239.

Natural variant

722

1

I → T Confers resistance to delavirdine, efavirenz and nevirapine; when associated with I-239.

Natural variant

725

1

E → K Confers resistance to emivirine.

Natural variant

732

1

Q → M Confers both multi-NRTI and multi-NNRTI resistance.

Natural variant

738

1

Q → M Confers multi-NRTI resistance; when associated with other amino acid changes.

Natural variant

743

1

S → A Confers resistance to pyrophosphate analog PFA.

Natural variant

744

1

P → S Confers resistance to lamivudine.

Natural variant

748

1

Q → L Confers resistance to pyrophosphate analog PFA.

Natural variant

766

1

V → D Confers resistance to efavirenz, tivirapine and trovirdine; when associated with other amino acid changes.

Natural variant

768

1

Y → C Confers multi-NNRTI resistance.

Natural variant

771

1

M → I Confers resistance to lamivudine and emtricitabine.

Natural variant

771

1

M → T Confers resistance to abacavir, didanosine, emtricitabine, lamivudine and zalcitabine.

Natural variant

771

1

M → V Confers resistance to lamivudine.

Natural variant

775

1

Y → C Confers resistance to nevirapine.

Natural variant

775

1

Y → H Confers resistance to atevirdine, efavirenz, loviride and zidovudine.

Natural variant

775

1

Y → L Confers resistance to efavirenz.

Natural variant

776

1

V → I Confers resistance to HBY 097.

Natural variant

777

1

G → A Confers resistance to efavirenz and nevirapine.

Natural variant

777

1

G → C Confers resistance to efavirenz and nevirapine.

Natural variant

777

1

G → E Confers resistance to efavirenz, nevirapine and quinoxaline.

Natural variant

777

1

G → Q Confers resistance to efavirenz, HBY 097 and nevirapine.

Natural variant

777

1

G → S Confers resistance to efavirenz and nevirapine.

Natural variant

777

1

G → T Confers resistance to efavirenz, HBY 097 and nevirapine.

Natural variant

777

1

G → V Confers resistance to efavirenz and nevirapine.

Natural variant

795

1

H → Y Confers resistance to lamivudine, pyrophosphate analog PFA and zidovudine.

Natural variant

797

1

L → W Confers resistance to zidovudine.

Natural variant

798

1

R → K Confers resistance to lamivudine and zidovudine.

Natural variant

801

1

L → F Confers resistance to ph-AZT and zidovudine.

Natural variant

802

1

T → F Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

802

1

T → Y Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

806

1

K → E Confers resistance to zidovudine.

Natural variant

806

1

K → Q Confers resistance to zidovudine; when associated with other amino acid changes.

Natural variant

806

1

K → R Confers resistance to lamivudine, stavudine, zalcicabine and zidovudine.

Natural variant

812

1

P → H Confers resistance to efavirenz, emivirine, HBY 097 and quinoxaline; when associated with A-17.

Natural variant

823

1

P → L Confers resistance to atevirdine and delavirdine.

Natural variant

825

1

K → T Confers resistance to atevirdine and zidovudine; when associated with other amino acid changes.

Natural variant

870

1

L → I Confers resistance to delavirdine, efavirenz and nevirapine.

Natural variant

905

1

Y → F Confers resistance to delavirdine and nevirapine.

Natural variant

920

1

G → D Confers resistance to abacavir, lamivudine and zidovudine.

Natural variant

920

1

G → E Confers resistance to abacavir, lamivudine and zidovudine.

Natural variant

973

1

T → I Confers resistance to abacavir, lamivudine and zidovudine.

Experimental info

Mutagenesis

217

1

P → A: 3-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

218

1

V → A: 2.7-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

219

1

H → A or Q: 8-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

220

1

A → G: 44-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

220

1

A → V: 3.4-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

221

1

G → A: 31-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

221

1

G → V: 154-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

222

1

P → A: 36-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

222

1

P → V: More than 150-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

223

1

I → A: 1.2-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

223

1

I → V: 1.0-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

224

1

A → G: 2.3-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

224

1

A → V: 1.7-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

225

1

P → A: 1.6-fold decrease of PPIA-binding affinity. Ref.9

Mutagenesis

394

1

N → F or G: Decreases infectivity and replication. Ref.21

Mutagenesis

400

1

H → C: Complete loss of infectivity and in vitro chaperone activity. Ref.15

Mutagenesis

405

1

C → H: Complete loss of infectivity and DNA synthesis. Ref.15

Mutagenesis

421

1

H → C: Partial loss of infectivity. Complete loss of in vitro chaperone activity. Ref.15

Mutagenesis

426

1

C → H: Partial loss of infectivity. Ref.15

Mutagenesis

1065

1

E → Q: Complete loss of RNase H activity. Ref.13

Mutagenesis

1136

1

D → N: Complete loss of RNase H activity. Ref.13

Mutagenesis

1159

1

H → C: No effect on integrase activity in vitro. Ref.4

Mutagenesis

1163

1

H → C or V: 75% increase of integrase activity in vitro. Ref.4

Mutagenesis

1187

1

C → A: Complete loss of integrase activity in vivo. Ref.5

Mutagenesis

1190

1

C → A: Complete loss of integrase activity in vivo. Ref.5

Mutagenesis

1200

1

Q → C: 75% increase of integrase activity in vitro. Ref.4

Mutagenesis

1208

1

W → A: Complete loss of integrase activity in vivo. Ref.5

Mutagenesis

1211

1

D → A or V: Complete loss of integrase activity in vivo and in vitro. Ref.4 Ref.5 Ref.10

Mutagenesis

1213

1

T → A: No effect on infectivity. Ref.5

Mutagenesis

1222

1

V → P: Complete loss of integrase activity. Ref.5

Mutagenesis

1228

1

S → A: Complete loss of integrase activity in vivo. Ref.4 Ref.5

Mutagenesis

1228

1

S → R: No effect on integrase activity in vitro. Ref.4 Ref.5

Mutagenesis

1262

1

T → A: No effect infectivity. Ref.5

Mutagenesis

1263

1

D → A or I: Complete loss of integrase activity in vivo and in vitro. Ref.4 Ref.5 Ref.10

Mutagenesis

1270

1

G → A: No effect on infectivity. Ref.5

Mutagenesis

1282

1

I → P: Complete loss of integrase activity in vivo. Ref.5

Mutagenesis

1298

1

V → A: No effect on infectivity. Ref.5

Mutagenesis

1299

1

E → G or P: Complete loss of integrase activity in vitro. Ref.4 Ref.5 Ref.10

Mutagenesis

1306

1

K → P: Slow down virus replication. Ref.5

Mutagenesis

1326

1

A → P: Complete loss of integrase activity in vivo. Ref.5

Mutagenesis

1346

1

R → C: 75% increase of integrase activity in vitro. Ref.4

Mutagenesis

1382

1

W → A: Complete loss of infectivity. No effect on integrase activity in vitro. Ref.4 Ref.5

Mutagenesis

1382

1

W → E: 75% increase of integrase activity in vitro. Ref.4 Ref.5

Secondary structure

1

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1435

Helix Strand Turn

Details...

Beta strand

393 – 395

3

Turn

402 – 404

3

Beta strand

414 – 416

3

Turn

423 – 425

3

Beta strand

493 – 495

3

Beta strand

498 – 503

6

Beta strand

506 – 512

7

Beta strand

516 – 518

3

Beta strand

520 – 523

4

Beta strand

531 – 537

7

Beta strand

540 – 554

15

Beta strand

557 – 566

10

Helix

575 – 578

4

Turn

579 – 582

4

Beta strand

584 – 586

3

Beta strand

594 – 599

6

Beta strand

602 – 607

6

Beta strand

610 – 616

7

Beta strand

635 – 641

7

Beta strand

644 – 658

15

Beta strand

661 – 670

10

Helix

679 – 682

4

Turn

683 – 686

4

Beta strand

691 – 697

7

Helix

699 – 701

3

Turn

702 – 704

3

Helix

711 – 715

5

Beta strand

717 – 719

3

Beta strand

729 – 735

7

Helix

743 – 761

19

Beta strand

765 – 770

6

Beta strand

773 – 778

6

Helix

782 – 798

17

Helix

806 – 808

3

Beta strand

812 – 816

5

Beta strand

819 – 822

4

Beta strand

825 – 828

4

Beta strand

837 – 840

4

Helix

841 – 854

14

Turn

855 – 857

3

Helix

864 – 868

5

Turn

869 – 872

4

Helix

884 – 896

13

Beta strand

913 – 920

8

Beta strand

923 – 931

9

Beta strand

934 – 942

9

Beta strand

947 – 949

3

Helix

951 – 970

20

Beta strand

975 – 980

6

Helix

982 – 991

10

Beta strand

993 – 995

3

Beta strand

1000 – 1003

4

Beta strand

1024 – 1034

11

Turn

1035 – 1038

4

Beta strand

1039 – 1046

8

Beta strand

1051 – 1058

8

Helix

1061 – 1076

16

Beta strand

1078 – 1084

7

Helix

1087 – 1095

9

Beta strand

1098 – 1101

4

Helix

1103 – 1114

12

Beta strand

1116 – 1122

7

Helix

1131 – 1140

10

Helix

1204 – 1206

3

Beta strand

1207 – 1215

9

Beta strand

1218 – 1225

8

Turn

1226 – 1228

3

Beta strand

1231 – 1240

10

Helix

1241 – 1254

14

Beta strand

1259 – 1261

3

Helix

1266 – 1268

3

Helix

1271 – 1280

10

Helix

1302 – 1312

11

Helix

1313 – 1315

3

Helix

1319 – 1332

14

Beta strand

1335 – 1339

5

Helix

1343 – 1355

13

Helix

1358 – 1368

11

Beta strand

1370 – 1374

5

Beta strand

1383 – 1391

9

Beta strand

1393 – 1399

7

Beta strand

1404 – 1408

5

Helix

1409 – 1411

3

Beta strand

1412 – 1414

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform Gag-Pol polyprotein [UniParc]. Last modified January 23, 2007. Version 4. Checksum: 8487B36BDEAC5FE4	FASTA	1,435	162,042
	10 20 30 40 50 60 MGARASVLSG GELDRWEKIR LRPGGKKKYK LKHIVWASRE LERFAVNPGL LETSEGCRQI 70 80 90 100 110 120 LGQLQPSLQT GSEELRSLYN TVATLYCVHQ RIEIKDTKEA LDKIEEEQNK SKKKAQQAAA 130 140 150 160 170 180 DTGHSNQVSQ NYPIVQNIQG QMVHQAISPR TLNAWVKVVE EKAFSPEVIP MFSALSEGAT 190 200 210 220 230 240 PQDLNTMLNT VGGHQAAMQM LKETINEEAA EWDRVHPVHA GPIAPGQMRE PRGSDIAGTT 250 260 270 280 290 300 STLQEQIGWM TNNPPIPVGE IYKRWIILGL NKIVRMYSPT SILDIRQGPK EPFRDYVDRF 310 320 330 340 350 360 YKTLRAEQAS QEVKNWMTET LLVQNANPDC KTILKALGPA ATLEEMMTAC QGVGGPGHKA 370 380 390 400 410 420 RVLAEAMSQV TNSATIMMQR GNFRNQRKIV KCFNCGKEGH TARNCRAPRK KGCWKCGKEG 430 440 450 460 470 480 HQMKDCTERQ ANFLREDLAF LQGKAREFSS EQTRANSPTR RELQVWGRDN NSPSEAGADR 490 500 510 520 530 540 QGTVSFNFPQ VTLWQRPLVT IKIGGQLKEA LLDTGADDTV LEEMSLPGRW KPKMIGGIGG 550 560 570 580 590 600 FIKVRQYDQI LIEICGHKAI GTVLVGPTPV NIIGRNLLTQ IGCTLNFPIS PIETVPVKLK 610 620 630 640 650 660 PGMDGPKVKQ WPLTEEKIKA LVEICTEMEK EGKISKIGPE NPYNTPVFAI KKKDSTKWRK 670 680 690 700 710 720 LVDFRELNKR TQDFWEVQLG IPHPAGLKKK KSVTVLDVGD AYFSVPLDED FRKYTAFTIP 730 740 750 760 770 780 SINNETPGIR YQYNVLPQGW KGSPAIFQSS MTKILEPFRK QNPDIVIYQY MDDLYVGSDL 790 800 810 820 830 840 EIGQHRTKIE ELRQHLLRWG LTTPDKKHQK EPPFLWMGYE LHPDKWTVQP IVLPEKDSWT 850 860 870 880 890 900 VNDIQKLVGK LNWASQIYPG IKVRQLCKLL RGTKALTEVI PLTEEAELEL AENREILKEP 910 920 930 940 950 960 VHGVYYDPSK DLIAEIQKQG QGQWTYQIYQ EPFKNLKTGK YARMRGAHTN DVKQLTEAVQ 970 980 990 1000 1010 1020 KITTESIVIW GKTPKFKLPI QKETWETWWT EYWQATWIPE WEFVNTPPLV KLWYQLEKEP 1030 1040 1050 1060 1070 1080 IVGAETFYVD GAANRETKLG KAGYVTNRGR QKVVTLTDTT NQKTELQAIY LALQDSGLEV 1090 1100 1110 1120 1130 1140 NIVTDSQYAL GIIQAQPDQS ESELVNQIIE QLIKKEKVYL AWVPAHKGIG GNEQVDKLVS 1150 1160 1170 1180 1190 1200 AGIRKVLFLD GIDKAQDEHE KYHSNWRAMA SDFNLPPVVA KEIVASCDKC QLKGEAMHGQ 1210 1220 1230 1240 1250 1260 VDCSPGIWQL DCTHLEGKVI LVAVHVASGY IEAEVIPAET GQETAYFLLK LAGRWPVKTI 1270 1280 1290 1300 1310 1320 HTDNGSNFTG ATVRAACWWA GIKQEFGIPY NPQSQGVVES MNKELKKIIG QVRDQAEHLK 1330 1340 1350 1360 1370 1380 TAVQMAVFIH NFKRKGGIGG YSAGERIVDI IATDIQTKEL QKQITKIQNF RVYYRDSRNP 1390 1400 1410 1420 1430 LWKGPAKLLW KGEGAVVIQD NSDIKVVPRR KAKIIRDYGK QMAGDDCVAS RQDED
	Isoform Gag polyprotein. See P04591.	FASTA	–	–

References

[1]	"Complete nucleotide sequences of functional clones of the AIDS virus." Ratner L., Fisher A., Jagodzinski L.L., Mitsuya H., Liou R.-S., Gallo R.C., Wong-Staal F. AIDS Res. Hum. Retroviruses 3:57-69(1987) [PubMed: 3040055] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]	Ogata N., Alter H.J., Miller R.H., Purcell R.H. Submitted (JUN-1996) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION.
[3]	Chappey C. Submitted (MAR-1999) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[4]	"Site-directed mutagenesis of HIV-1 integrase demonstrates differential effects on integrase functions in vitro." Leavitt A.D., Shiue L., Varmus H.E. J. Biol. Chem. 268:2113-2119(1993) [PubMed: 8420982] [Abstract] Cited for: MUTAGENESIS OF HIS-1159; HIS-1163; GLN-1200; ASP-1211; SER-1228; ASP-1263; GLU-1299; ARG-1346 AND TRP-1382.
[5]	"Human immunodeficiency virus type 1 integrase: effect on viral replication of mutations at highly conserved residues." Cannon P.M., Wilson W., Byles E., Kingsman S.M., Kingsman A.J. J. Virol. 68:4768-4775(1994) [PubMed: 8035478] [Abstract] Cited for: MUTAGENESIS OF CYS-1187; CYS-1190; TRP-1208; ASP-1211; THR-1213; VAL-1222; SER-1228; THR-1262; ASP-1263; GLY-1270; ILE-1282; VAL-1298; GLU-1299; LYS-1306; ALA-1326 AND TRP-1382. Strain: Isolate WI3.
[6]	"Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B." Luban J., Bossolt K.L., Franke E.K., Kalpana G.V., Goff S.P. Cell 73:1067-1078(1993) [PubMed: 8513493] [Abstract] Cited for: INTERACTION OF CAPSID WITH HUMAN PPIA/CYPA.
[7]	"Binding and stimulation of HIV-1 integrase by a human homolog of yeast transcription factor SNF5." Kalpana G.V., Marmon S., Wang W., Crabtree G.R., Goff S.P. Science 266:2002-2006(1994) [PubMed: 7801128] [Abstract] Cited for: INTERACTION OF INTEGRASE WITH HUMAN SMARCB1/INI1.
[8]	"Cyclophilin A is required for an early step in the life cycle of human immunodeficiency virus type 1 before the initiation of reverse transcription." Braaten D., Franke E.K., Luban J. J. Virol. 70:3551-3560(1996) [PubMed: 8648689] [Abstract] Cited for: FUNCTION OF CAPSID.
[9]	"Molecular recognition in the HIV-1 capsid/cyclophilin A complex." Yoo S., Myszka D.G., Yeh C., McMurray M., Hill C.P., Sundquist W.I. J. Mol. Biol. 269:780-795(1997) [PubMed: 9223641] [Abstract] Cited for: MUTAGENESIS OF PRO-217; VAL-218; HIS-219; ALA-220; GLY-221; PRO-222; ILE-223; ALA-224 AND PRO-225.
[10]	"Mutations in the human immunodeficiency virus type 1 integrase D,D(35)E motif do not eliminate provirus formation." Gaur M., Leavitt A.D. J. Virol. 72:4678-4685(1998) [PubMed: 9573231] [Abstract] Cited for: MUTAGENESIS OF ASP-1211; ASP-1263 AND GLU-1299.
[11]	"Organization of HIV-1 pol is critical for Pol polyprotein processing." Chang Y.Y., Yu S.L., Syu W.J. J. Biomed. Sci. 6:333-341(1999) [PubMed: 10494040] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[12]	"Maintenance of the Gag/Gag-Pol ratio is important for human immunodeficiency virus type 1 RNA dimerization and viral infectivity." Shehu-Xhilaga M., Crowe S.M., Mak J. J. Virol. 75:1834-1841(2001) [PubMed: 11160682] [Abstract] Cited for: GAG/GAG-POL RATIO.
[13]	"Mutations in the ribonuclease H active site of HIV-RT reveal a role for this site in stabilizing enzyme-primer-template binding." Cristofaro J.V., Rausch J.W., Le Grice S.F., DeStefano J.J. Biochemistry 41:10968-10975(2002) [PubMed: 12206668] [Abstract] Cited for: ACTIVE SITES OF RNASE H, MUTAGENESIS OF GLU-1065 AND ASP-1136.
[14]	"Catalysis of cis/trans isomerization in native HIV-1 capsid by human cyclophilin A." Bosco D.A., Eisenmesser E.Z., Pochapsky S., Sundquist W.I., Kern D. Proc. Natl. Acad. Sci. U.S.A. 99:5247-5252(2002) [PubMed: 11929983] [Abstract] Cited for: CIS/TRANS ISOMERIZATION OF CAPSID.
[15]	"Subtle alterations of the native zinc finger structures have dramatic effects on the nucleic acid chaperone activity of human immunodeficiency virus type 1 nucleocapsid protein." Guo J., Wu T., Kane B.F., Johnson D.G., Henderson L.E., Gorelick R.J., Levin J.G. J. Virol. 76:4370-4378(2002) [PubMed: 11932404] [Abstract] Cited for: MUTAGENESIS OF HIS-400; CYS-405; HIS-421 AND CYS-426.
[16]	"The dimer interfaces of protease and extra-protease domains influence the activation of protease and the specificity of GagPol cleavage." Pettit S.C., Gulnik S., Everitt L., Kaplan A.H. J. Virol. 77:366-374(2003) [PubMed: 12477841] [Abstract] Cited for: PROTEOLYTIC PROCESSING OF POLYPROTEIN.
[17]	"The barrier-to-autointegration factor is a component of functional human immunodeficiency virus type 1 preintegration complexes." Lin C.W., Engelman A. J. Virol. 77:5030-5036(2003) [PubMed: 12663813] [Abstract] Cited for: INTERACTION OF MATRIX PROTEIN P17 WITH HUMAN BAF.
[18]	"Structural organization of authentic, mature HIV-1 virions and cores." Briggs J.A., Wilk T., Welker R., Krausslich H.G., Fuller S.D. EMBO J. 22:1707-1715(2003) [PubMed: 12660176] [Abstract] Cited for: QUARTERNARY STRUCTURE OF CAPSID.
[19]	"In vitro processing of HIV-1 nucleocapsid protein by the viral proteinase: effects of amino acid substitutions at the scissile bond in the proximal zinc finger sequence." Tozser J., Shulenin S., Louis J.M., Copeland T.D., Oroszlan S. Biochemistry 43:4304-4312(2004) [PubMed: 15065874] [Abstract] Cited for: CLEAVAGE OF NUCLEOCAPSID PROTEIN P7.
[20]	"Human immunodeficiency virus type 1 Gag polyprotein modulates its own translation." Anderson E.C., Lever A.M. J. Virol. 80:10478-10486(2006) [PubMed: 17041220] [Abstract] Cited for: FUNCTION.
[21]	"Characterization of human immunodeficiency virus type 1 (HIV-1) containing mutations in the nucleocapsid protein at a putative HIV-1 protease cleavage site." Thomas J.A., Shulenin S., Coren L.V., Bosche W.J., Gagliardi T.D., Gorelick R.J., Oroszlan S. Virology 354:261-270(2006) [PubMed: 16904152] [Abstract] Cited for: MUTAGENESIS OF ASN-394.
[22]	"Dissecting the protein-RNA and RNA-RNA interactions in the nucleocapsid-mediated dimerization and isomerization of HIV-1 stemloop 1." Hagan N.A., Fabris D. J. Mol. Biol. 365:396-410(2007) [PubMed: 17070549] [Abstract] Cited for: FUNCTION OF NUCLEOCAPSID PROTEIN P7.
[23]	"Human cell proteins and human immunodeficiency virus DNA integration." Turlure F., Devroe E., Silver P.A., Engelman A. Front. Biosci. 9:3187-3208(2004) [PubMed: 15353349] [Abstract] Cited for: REVIEW.
[24]	"Evidence that HIV-1 reverse transcriptase employs the DNA 3' end directed primary/secondary RNase H cleavage mechanism during synthesis and strand transfer." Purohit V., Balakrishnan M., Kim B., Bambara R.A. J. Biol. Chem. 280:40534-40543(2005) [PubMed: 16221683] [Abstract] Cited for: CHARACTERIZATION OF REVERSE TRANSCRIPTASE AND RNASE H.
[25]	"Proteolytic processing and particle maturation." Vogt V.M. Curr. Top. Microbiol. Immunol. 214:95-131(1996) [PubMed: 8791726] [Abstract] Cited for: REVIEW.
[26]	"Structural biology of HIV." Turner B.G., Summers M.F. J. Mol. Biol. 285:1-32(1999) [PubMed: 9878383] [Abstract] Cited for: REVIEW.
[27]	"Mechanisms of retroviral recombination." Negroni M., Buc H. Annu. Rev. Genet. 35:275-302(2001) [PubMed: 11700285] [Abstract] Cited for: REVIEW.
[28]	"Retroviral proteases." Dunn B.M., Goodenow M.M., Gustchina A., Wlodawer A. Genome Biol. 3:REVIEWS3006.1-REVIEWS3006.7(2002) [PubMed: 11983066] [Abstract] Cited for: REVIEW.
[29]	"Role of HIV-1 Gag domains in viral assembly." Scarlata S., Carter C. Biochim. Biophys. Acta 1614:62-72(2003) [PubMed: 12873766] [Abstract] Cited for: REVIEW.
[30]	"Cyclophilin, TRIM5, and innate immunity to HIV-1." Sokolskaja E., Luban J. Curr. Opin. Microbiol. 9:404-408(2006) [PubMed: 16815734] [Abstract] Cited for: REVIEW.
[31]	"X-ray analysis of HIV-1 proteinase at 2.7-A resolution confirms structural homology among retroviral enzymes." Lapatto R., Blundell T., Hemmings A., Overington J., Wilderspin A., Wood S., Merson J.R., Whittle P.J., Danley D.E., Geoghegan K.F., Hawrylik S.J., Lee S.E., Scheld K.G., Hobart P.M. Nature 342:299-302(1989) [PubMed: 2682266] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 489-587.
[32]	"Novel binding mode of highly potent HIV-proteinase inhibitors incorporating the (R)-hydroxyethylamine isostere." Krohn A., Redshaw S., Ritchie J.C., Graves B.J., Hatada M.H. J. Med. Chem. 34:3340-3342(1991) [PubMed: 1956054] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 489-587 IN COMPLEX WITH THE INHIBITOR RO 32-8959.
[33]	"Structural characterization of a 39-residue synthetic peptide containing the two zinc binding domains from the HIV-1 p7 nucleocapsid protein by CD and NMR spectroscopy." Omichinski J.G., Clore G.M., Sakaguchi K., Appella E., Gronenborn A.M. FEBS Lett. 292:25-30(1991) [PubMed: 1959614] [Abstract] Cited for: STRUCTURE BY NMR OF 390-406.
[34]	"Crystal structure of a complex of HIV-1 protease with a dihydroxyethylene-containing inhibitor: comparisons with molecular modeling." Thanki N., Rao J.K., Foundling S.I., Howe W.J., Moon J.B., Hui J.O., Tomasselli A.G., Heinrikson R.L., Thaisrivongs S., Wlodawer A. Protein Sci. 1:1061-1072(1992) [PubMed: 1304383] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 489-587 IN COMPLEX WITH A DIHYDROXYETHYLENE-CONTAINING INHIBITOR.
[35]	"Conformational behaviour of the active and inactive forms of the nucleocapsid NCp7 of HIV-1 studied by 1H NMR." Morellet N., de Rocquigny H., Mely Y., Jullian N., Demene H., Ottmann M., Gerard D., Darlix J.L., Fournie-Zaluski M.-C., Roques B.P. J. Mol. Biol. 235:287-301(1994) [PubMed: 8289249] [Abstract] Cited for: STRUCTURE BY NMR OF 390-430.
[36]	"Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors." Lam P.Y.S., Jadhav P.K., Eyermann C.J., Hodge C.N., Ru Y., Bacheler L.T., Meek J.L., Otto M.J., Rayner M.M., Wong Y.N., Chang C.-H., Weber P.C., Jackson D.A., Sharpe T.R., Erickson-Viitanen S. Science 263:380-384(1994) [PubMed: 8278812] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 489-587 IN COMPLEX WITH THE INHIBITOR XK263.
[37]	"Crystals of HIV-1 reverse transcriptase diffracting to 2.2 A resolution." Stammers D.K., Somers D.O., Ross C.K., Kirby I., Ray P.H., Wilson J.E., Norman M., Ren J.S., Esnouf R.M., Garman E.F., Jones E.Y., Stuart D.I. J. Mol. Biol. 242:586-588(1994) [PubMed: 7523679] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 588-1147.
[38]	"Refined solution structure of p17, the HIV matrix protein." Matthews S., Barlow P., Clark N., Kingsman S., Kingsman A., Campbell I. Biochem. Soc. Trans. 23:725-729(1995) [PubMed: 8654825] [Abstract] Cited for: STRUCTURE BY NMR OF 1-132.
[39]	"The structure of HIV-1 reverse transcriptase complexed with 9-chloro-TIBO: lessons for inhibitor design." Ren J.S., Esnouf R.M., Hopkins A.L., Ross C.K., Jones E.Y., Stammers D.K., Stuart D.I. Structure 3:915-926(1995) [PubMed: 8535785] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 588-1027.
[40]	"Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors." Esnouf R.M., Ren J.S., Ross C.K., Jones E.Y., Stammers D.K., Stuart D.I. Nat. Struct. Biol. 2:303-308(1995) [PubMed: 7540935] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 588-1147.
[41]	"Complexes of HIV-1 reverse transcriptase with inhibitors of the HEPT series reveal conformational changes relevant to the design of potent non-nucleoside inhibitors." Hopkins A.L., Ren J.S., Esnouf R.M., Willcox B.E., Jones E.Y., Ross C.K., Miyasaka T., Walker R.T., Tanaka H., Stammers D.K., Stuart D.I. J. Med. Chem. 39:1589-1600(1996) [PubMed: 8648598] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF 588-1027.
[42]	"Improved cyclic urea inhibitors of the HIV-1 protease: synthesis, potency, resistance profile, human pharmacokinetics and X-ray crystal structure of DMP 450." Hodge C.N., Aldrich P.E., Bacheler L.T., Chang C.-H., Eyermann C.J., Garber S.S., Grubb M., Jackson D.A., Jadhav P.K., Korant B.D., Lam P.Y.S., Maurin M.B., Meek J.L., Otto M.J., Rayner M.M., Reid C., Sharpe T.R., Shum L., Winslow D.L., Erickson-Viitanen S. Chem. Biol. 3:301-314(1996) [PubMed: 8807858] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 489-587 IN COMPLEX WITH COMPLEX WITH DMP450.
[43]	"Three-dimensional solution structure of the HIV-1 protease complexed with DMP323, a novel cyclic urea-type inhibitor, determined by nuclear magnetic resonance spectroscopy." Yamazaki T., Hinck A.P., Wang Y.X., Nicholson L.K., Torchia D.A., Wingfield P., Stahl S.J., Kaufman J.D., Chang C.-H., Domaille P.J., Lam P.Y.S. Protein Sci. 5:495-506(1996) [PubMed: 8868486] [Abstract] Cited for: STRUCTURE BY NMR OF 489-587 IN COMPLEX WITH THE INHIBITOR DMP323.
[44]	"Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (BHAP) U-90152 explain resistance mutations for this nonnucleoside inhibitor." Esnouf R.M., Ren J.S., Hopkins A.L., Ross C.K., Jones E.Y., Stammers D.K., Stuart D.I. Proc. Natl. Acad. Sci. U.S.A. 94:3984-3989(1997) [PubMed: 9108091] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.65 ANGSTROMS) OF 588-1130.
[45]	"Cyclic urea amides: HIV-1 protease inhibitors with low nanomolar potency against both wild type and protease inhibitor resistant mutants of HIV." Jadhav P.K., Ala P.J., Woerner F.J., Chang C.-H., Garber S.S., Anton E.D., Bacheler L.T. J. Med. Chem. 40:181-191(1997) [PubMed: 9003516] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 489-587.
[46]	"Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV." Kervinen J., Lubkowski J., Zdanov A., Bhatt D., Dunn B.M., Hui K.Y., Powell D.J., Kay J., Wlodawer A., Gustchina A. Protein Sci. 7:2314-2323(1998) [PubMed: 9827997] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 489-587 IN COMPLEX WITH THE INHIBITOR LP-130.
[47]	"Nonpeptide cyclic cyanoguanidines as HIV-1 protease inhibitors: synthesis, structure-activity relationships, and X-ray crystal structure studies." Jadhav P.K., Woerner F.J., Lam P.Y., Hodge C.N., Eyermann C.J., Man H.W., Daneker W.F., Bacheler L.T., Rayner M.M., Meek J.L., Erickson-Viitanen S., Jackson D.A., Calabrese J.C., Schadt M.C., Chang C.-H. J. Med. Chem. 41:1446-1455(1998) [PubMed: 9554878] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 489-587.
[48]	"Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities." Ala P.J., Huston E.E., Klabe R.M., Jadhav P.K., Lam P.Y.S., Chang C.-H. Biochemistry 37:15042-15049(1998) [PubMed: 9790666] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 489-587.
[49]	"Molecular recognition of cyclic urea HIV-1 protease inhibitors." Ala P.J., DeLoskey R.J., Huston E.E., Jadhav P.K., Lam P.Y.S., Eyermann C.J., Hodge C.N., Schadt M.C., Lewandowski F.A., Weber P.C., McCabe D.D., Duke J.L., Chang C.-H. J. Biol. Chem. 273:12325-12331(1998) [PubMed: 9575185] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 489-587.
[50]	"Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease." Louis J.M., Dyda F., Nashed N.T., Kimmel A.R., Davies D.R. Biochemistry 37:2105-2110(1998) [PubMed: 9485357] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 490-587 IN COMPLEX WITH A TRIPEPTIDE INHIBITOR.
[51]	"3'-azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes." Ren J.S., Esnouf R.M., Hopkins A.L., Jones E.Y., Kirby I., Keeling J., Ross C.K., Larder B.A., Stuart D.I., Stammers D.K. Proc. Natl. Acad. Sci. U.S.A. 95:9518-9523(1998) [PubMed: 9689112] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 588-1130.
[52]	"Crystal structures of HIV-1 reverse transcriptase in complex with carboxanilide derivatives." Ren J.S., Esnouf R.M., Hopkins A.L., Warren J., Balzarini J., Stuart D.I., Stammers D.K. Biochemistry 37:14394-14403(1998) [PubMed: 9772165] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 588-1147 IN COMPLEX WITH CARBOXANILIDE DERIVATIVES.
[53]	"Structural and kinetic analysis of drug resistant mutants of HIV-1 protease." Mahalingam B., Louis J.M., Reed C.C., Adomat J.M., Krouse J., Wang Y.-F., Harrison R.W., Weber I.T. Eur. J. Biochem. 263:238-245(1999) [PubMed: 10429209] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) OF 501-599.
[54]	"Crystal structure of the HIV-1 integrase catalytic core and C-terminal domains: a model for viral DNA binding." Chen J.C., Krucinski J., Miercke L.J., Finer-Moore J.S., Tang A.H., Leavitt A.D., Stroud R.M. Proc. Natl. Acad. Sci. U.S.A. 97:8233-8238(2000) [PubMed: 10890912] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1199-1435.
[55]	"1.9 A X-ray study shows closed flap conformation in crystals of tethered HIV-1 PR." Pillai B., Kannan K.K., Hosur M.V. Proteins 43:57-64(2001) [PubMed: 11170214] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 489-587.
[56]	"Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors." Ren J.S., Nichols C.E., Bird L.E., Chamberlain P.P., Weaver K.L., Short S.A., Stuart D.I., Stammers D.K. J. Mol. Biol. 312:795-805(2001) [PubMed: 11575933] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 588-1147 IN COMPLEX WITH INHIBITORS.
[57]	"Effects of remote mutation on the autolysis of HIV-1 PR: X-ray and NMR investigations." Kumar M., Kannan K.K., Hosur M.V., Bhavesh N.S., Chatterjee A., Mittal R., Hosur R.V. Biochem. Biophys. Res. Commun. 294:395-401(2002) [PubMed: 12051725] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 489-587.
[58]	"Solution structure of the RNase H domain of the HIV-1 reverse transcriptase in the presence of magnesium." Pari K., Mueller G.A., DeRose E.F., Kirby T.W., London R.E. Biochemistry 42:639-650(2003) [PubMed: 12534276] [Abstract] Cited for: STRUCTURE BY NMR OF 1014-1147.
[59]	"Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors." Ren J.S., Nichols C.E., Chamberlain P.P., Weaver K.L., Short S.A., Stammers D.K. J. Mol. Biol. 336:569-578(2004) [PubMed: 15095972] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 588-1147 IN COMPLEX WITH INHIBITORS.
[60]	"Design of non-nucleoside inhibitors of HIV-1 reverse transcriptase with improved drug resistance properties. 2." Freeman G.A., Andrews C.W. III, Hopkins A.L., Lowell G.S., Schaller L.T., Cowan J.R., Gonzales S.S., Koszalka G.W., Hazen R.J., Boone L.R., Ferris R.G., Creech K.L., Roberts G.B., Short S.A., Weaver K.L., Reynolds D.J., Milton J., Ren J.S. , Stuart D.I., Stammers D.K., Chan J.H. J. Med. Chem. 47:5923-5936(2004) [PubMed: 15537347] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 588-1147 IN COMPLEX WITH INHIBITORS.
+	Additional computationally mapped references.

Web resources

HIV drug resistance mutations

hivdb

HIV drug resistance database

BioAfrica HIV proteomics resource

Pol entry

BioAfrica HIV proteomics resource

RT (p51) entry

BioAfrica HIV proteomics resource

RNase H (p15) entry

BioAfrica HIV proteomics resource

PR (p15) entry

BioAfrica HIV proteomics resource

IN (p31) entry

BioAfrica: HIV bioinformatics in Africa

Cross-references

Sequence databases

EMBLGenBankDDBJ

K03455 Genomic RNA. Translation: AAB50259.1. Sequence problems.
AF033819 Genomic RNA. Translation: AAC82598.2. Sequence problems.

RefSeq

NP_057849.4.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1A30	X-ray	2.00	A/B	489-587	[»]
1BV7	X-ray	2.00	A/B	489-587	[»]
1BV9	X-ray	2.00	A/B	489-587	[»]
1BVE	NMR	-	A/B	489-587	[»]
1BVG	NMR	-	A/B	489-587	[»]
1BWA	X-ray	1.90	A/B	489-587	[»]
1BWB	X-ray	1.80	A/B	489-587	[»]
1C0T	X-ray	2.70	A	588-1147	[»]
			B	588-1027	[»]
1C0U	X-ray	2.52	A	588-1147	[»]
			B	588-1027	[»]
1C1B	X-ray	2.50	A	588-1147	[»]
			B	588-1027	[»]
1C1C	X-ray	2.50	A	588-1147	[»]
			B	588-1027	[»]
1DMP	X-ray	2.00	A/B	489-587	[»]
1DTQ	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1DTT	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1E6J	X-ray	3.00	P	143-352	[»]
1EP4	X-ray	2.50	A	588-1147	[»]
			B	588-1027	[»]
1ESK	NMR	-	A	390-430	[»]
1EX4	X-ray	2.80	A/B	1199-1435	[»]
1EXQ	X-ray	1.60	A/B	1204-1356	[»]
1FB7	X-ray	2.60	A	489-587	[»]
1FK9	X-ray	2.50	A	588-1130	[»]
			B	588-1027	[»]
1FKO	X-ray	2.90	A	588-1130	[»]
			B	588-1027	[»]
1FKP	X-ray	2.90	A	588-1130	[»]
			B	588-1027	[»]
1G6L	X-ray	1.90	A	489-686	[»]
1HIV	X-ray	2.00	A/B	58-156	[»]
1HVH	X-ray	1.80	A/B	489-587	[»]
1HVR	X-ray	1.80	A/B	489-587	[»]
1HWR	X-ray	1.80	A/B	489-587	[»]
1HXB	X-ray	2.30	A/B	489-587	[»]
1JKH	X-ray	2.50	A	588-1147	[»]
			B	588-1027	[»]
1JLA	X-ray	2.50	A	588-1147	[»]
			B	588-1027	[»]
1JLB	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1JLC	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1JLE	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1JLF	X-ray	2.60	A	588-1147	[»]
			B	588-1027	[»]
1JLG	X-ray	2.60	A	588-1147	[»]
			B	588-1027	[»]
1JLQ	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1KLM	X-ray	2.65	A	588-1147	[»]
			B	588-1027	[»]
1LV1	X-ray	2.10	A	489-686	[»]
1LW0	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1LW2	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1LWC	X-ray	2.62	A	588-1147	[»]
			B	588-1027	[»]
1LWE	X-ray	2.81	A	588-1147	[»]
			B	588-1027	[»]
1LWF	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1NCP	NMR	-	N	390-406	[»]
1O1W	NMR	-	A	1014-1147	[»]
1ODW	X-ray	2.10	A/B	489-587	[»]
1ODY	X-ray	2.00	A/B	489-587	[»]
1QBR	X-ray	1.80	A/B	489-587	[»]
1QBS	X-ray	1.80	A/B	489-587	[»]
1QBT	X-ray	2.10	A/B	489-587	[»]
1QBU	X-ray	1.80	A/B	489-587	[»]
1REV	X-ray	2.60	A	588-1147	[»]
			B	588-1027	[»]
1RT1	X-ray	2.55	A	588-1147	[»]
			B	588-1027	[»]
1RT2	X-ray	2.55	A	588-1147	[»]
			B	588-1027	[»]
1RT3	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1RT4	X-ray	2.90	A	588-1147	[»]
			B	588-1027	[»]
1RT5	X-ray	2.90	A	588-1147	[»]
			B	588-1027	[»]
1RT6	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1RT7	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1RTD	X-ray	3.20	B/D	588-1027	[»]
1RTH	X-ray	2.20	A	588-1147	[»]
			B	588-1027	[»]
1RTI	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1RTJ	X-ray	2.35	A	588-1147	[»]
			B	588-1027	[»]
1S1T	X-ray	2.40	A	588-1147	[»]
			B	588-1027	[»]
1S1U	X-ray	3.00	A	588-1147	[»]
			B	588-1027	[»]
1S1V	X-ray	2.60	A	588-1147	[»]
			B	588-1027	[»]
1S1W	X-ray	2.70	A	588-1147	[»]
			B	588-1027	[»]
1S1X	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1T05	X-ray	3.00	B	588-1016	[»]
1TAM	NMR	-	A	1-132	[»]
1TKT	X-ray	2.60	A	588-1147	[»]
			B	588-1027	[»]
1TKX	X-ray	2.85	A	588-1147	[»]
			B	588-1027	[»]
1TKZ	X-ray	2.81	A	588-1147	[»]
			B	588-1027	[»]
1TL1	X-ray	2.90	A	588-1147	[»]
			B	588-1027	[»]
1TL3	X-ray	2.80	A	588-1147	[»]
			B	588-1027	[»]
1VRT	X-ray	2.20	A	588-1147	[»]
			B	588-1027	[»]
1VRU	X-ray	2.40	A	588-1147	[»]
			B	588-1027	[»]
2HND	X-ray	2.50	A	591-1124	[»]
			B	594-1015	[»]
2HNY	X-ray	2.50	A	591-1124	[»]
			B	594-1015	[»]
2HNZ	X-ray	3.00	A	591-1124	[»]
			B	594-1015	[»]
2NPH	X-ray	1.65	A/B	489-587	[»]
2OPP	X-ray	2.55	A	591-1132	[»]
			B	592-1018	[»]
2OPQ	X-ray	2.80	A	591-1124	[»]
			B