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P12495 (GAG_HV1Z2) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 130. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Gag polyprotein
Alternative name(s):
Pr55Gag

Cleaved into the following 6 chains:

  1. Matrix protein p17
    Short name=MA
  2. Capsid protein p24
    Short name=CA
  3. Spacer peptide p2
  4. Nucleocapsid protein p7
    Short name=NC
  5. Spacer peptide p1
  6. p6-gag
Gene names
Name:gag
OrganismHuman immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
Taxonomic identifier11683 [NCBI]
Taxonomic lineageVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostHomo sapiens (Human) [TaxID: 9606]

Protein attributes

Sequence length501 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu.

Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex.

Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers.

p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 By similarity.

Subunit structure

Matrix protein p17, and probably Pr55Gag form hexamer rings of trimers. Oligomerization possibly creates a central hole into which the cytoplasmic tail of the gp41 envelope protein may be inserted. Pr55Gag interacts with host TRIM22; this interaction seems to disrupt proper trafficking of Gag polyprotein and may interfere with budding. p6-gag interacts with Vpr. p6-gag interacts with host TSG101. p6-gag interacts with host PDCD6IP/AIP1 By similarity. Pr55Gag interacts with host PDZD8 By similarity.

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.

Domain

Late-budding domains (L domains) are short sequence motifs essential for viral particle budding. They recruit proteins of the host ESCRT machinery (Endosomal Sorting Complex Required for Transport) or ESCRT-associated proteins. p6-gag contains two L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 and a LYPX(n)L motif which interacts with PDCD6IP/AIP1 By similarity.

Post-translational modification

Capsid protein p24 is phosphorylated.

Specific enzymatic cleavages by the viral protease yield mature proteins. The polyprotein is cleaved during and after budding, this process is termed maturation By similarity.

Nucleocapsid protein p7 is methylated by host PRMT6, impairing its function by reducing RNA annealing and the initiation of reverse transcription By similarity.

Miscellaneous

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).

Sequence similarities

Belongs to the primate lentivirus group gag polyprotein family.

Contains 2 CCHC-type zinc fingers.

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 polyprotein (identifier: P12495-1)

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 conventional translation.
Isoform Gag-Pol polyprotein (identifier: P12499-1)

The sequence of this isoform can be found in the external entry P12499.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed; by host By similarity
Chain2 – 501500Gag polyprotein
PRO_0000261239
Chain2 – 133132Matrix protein p17 By similarity
PRO_0000038499
Chain134 – 364231Capsid protein p24 By similarity
PRO_0000038500
Peptide365 – 37915Spacer peptide p2 By similarity
PRO_0000038501
Chain380 – 43455Nucleocapsid protein p7 By similarity
PRO_0000038502
Peptide435 – 45016Spacer peptide p1 By similarity
PRO_0000038503
Chain451 – 50151p6-gag By similarity
PRO_0000038504

Regions

Zinc finger392 – 40918CCHC-type 1
Zinc finger413 – 43018CCHC-type 2
Motif16 – 227Nuclear export signal By similarity
Motif26 – 327Nuclear localization signal By similarity
Motif457 – 4604PTAP/PSAP motif
Motif484 – 49310LYPX(n)L motif

Sites

Site133 – 1342Cleavage; by viral protease By similarity
Site364 – 3652Cleavage; by viral protease By similarity
Site379 – 3802Cleavage; by viral protease By similarity
Site434 – 4352Cleavage; by viral protease By similarity
Site450 – 4512Cleavage; by viral protease By similarity

Amino acid modifications

Modified residue3891Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6 By similarity
Modified residue4111Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6 By similarity
Lipidation21N-myristoyl glycine; by host By similarity

Secondary structure

... 501
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Gag polyprotein [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: 827C2609BC3E5963

FASTA50155,678
        10         20         30         40         50         60 
MGARASVLSG GKLDAWEKIR LRPGGKKKYR LKHLVWASRE LERFALNPGL LETSDGCKQI 

        70         80         90        100        110        120 
IGQLQPAIRT GSEELRSLFN TVATLYCVHE RIEVKDTKEA LEKMEEEQNK SKNKKAQQAA 

       130        140        150        160        170        180 
ADAGNNSQVS QNYPIVQNLQ GQMVHQAISP RTLNAWVKVI EEKAFSPEVI PMFSALSEGA 

       190        200        210        220        230        240 
TPQDLNTMLN TVGGHQAAMQ MLKETINEEA AEWDRLHPVH AGPIAPGQMR EPRGSDIAGT 

       250        260        270        280        290        300 
TSTLQEQIAW MTSNPPIPVG EIYKRWIILG LNKIVRMYSP VSILDIRQGP KEPFRDYVDR 

       310        320        330        340        350        360 
FYKTLRAEQA SQEVKGWMTE TLLVQNANPD CKTILKALGP QATLEEMMTA CQGVGGPSHK 

       370        380        390        400        410        420 
ARVLAEAMSQ ATNSAAAVMM QRGNFKGPRK TIKCFNCGKE GHIAKNCRAP RRKGCWKCGK 

       430        440        450        460        470        480 
EGHQLKDCTE RQANFLGKIW PSHKGRPGNF LQSRPEPTAP PAESFGFGEE ITPSQKQEQK 

       490        500 
DKELYPSTAL KSLFGNDPLL Q 

« Hide

Isoform Gag-Pol polyprotein [UniParc].

See P12499.

References

[1]Theodore T., Buckler-White A.J.
Submitted (JUL-1989) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC RNA].
[2]"Role of HIV-1 Gag domains in viral assembly."
Scarlata S., Carter C.
Biochim. Biophys. Acta 1614:62-72(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M22639 Genomic RNA. Translation: AAA45365.1.
PIRS54377.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1SJEX-ray2.45C167-182[»]
1SJHX-ray2.25C167-179[»]
3D3TX-ray2.80P446-455[»]
ProteinModelPortalP12495.
SMRP12495. Positions 2-434, 451-501.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.
InterProIPR000721. Gag_p24.
IPR014817. Gag_p6.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_N_HIV/RSV.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix_N.
IPR001878. Znf_CCHC.
[Graphical view]
PfamPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF08705. Gag_p6. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSPR00234. HIV1MATRIX.
SMARTSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMSSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEPS50158. ZF_CCHC. 2 hits.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP12495.

Entry information

Entry nameGAG_HV1Z2
AccessionPrimary (citable) accession number: P12495
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: January 23, 2007
Last modified: February 19, 2014
This is version 130 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references