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P12495

- GAG_HV1Z2

UniProt

P12495 - GAG_HV1Z2

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Protein

Gag polyprotein

Gene

gag

Organism
Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei133 – 1342Cleavage; by viral proteaseBy similarity
Sitei364 – 3652Cleavage; by viral proteaseBy similarity
Sitei379 – 3802Cleavage; by viral proteaseBy similarity
Sitei434 – 4352Cleavage; by viral proteaseBy similarity
Sitei450 – 4512Cleavage; by viral proteaseBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri392 – 40918CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri413 – 43018CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW
  2. structural molecule activity Source: InterPro
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. viral budding via host ESCRT complex Source: UniProtKB-KW
  2. viral release from host cell Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, Viral budding, Viral budding via the host ESCRT complexes, Virus exit from host cell

Keywords - Ligandi

Metal-binding, RNA-binding, Viral nucleoprotein, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Gag polyprotein
Alternative name(s):
Pr55Gag
Cleaved into the following 6 chains:
Gene namesi
Name:gag
OrganismiHuman immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) (HIV-1)
Taxonomic identifieri11683 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]

Subcellular locationi

Chain Matrix protein p17 : Virion Curated. Host nucleus By similarity. Host cytoplasm By similarity. Host cell membrane Curated; Lipid-anchor Curated
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).By similarity

GO - Cellular componenti

  1. host cell cytoplasm Source: UniProtKB-KW
  2. host cell nucleus Source: UniProtKB-KW
  3. host cell plasma membrane Source: UniProtKB-KW
  4. membrane Source: UniProtKB-KW
  5. viral nucleocapsid Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Capsid protein, Host cell membrane, Host cytoplasm, Host membrane, Host nucleus, Membrane, Virion

Pathology & Biotechi

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed; by hostBy similarity
Chaini2 – 501500Gag polyproteinPRO_0000261239Add
BLAST
Chaini2 – 133132Matrix protein p17By similarityPRO_0000038499Add
BLAST
Chaini134 – 364231Capsid protein p24By similarityPRO_0000038500Add
BLAST
Peptidei365 – 37915Spacer peptide p2By similarityPRO_0000038501Add
BLAST
Chaini380 – 43455Nucleocapsid protein p7By similarityPRO_0000038502Add
BLAST
Peptidei435 – 45016Spacer peptide p1By similarityPRO_0000038503Add
BLAST
Chaini451 – 50151p6-gagBy similarityPRO_0000038504Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
Modified residuei389 – 3891Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6By similarity
Modified residuei411 – 4111Asymmetric dimethylarginine; in Nucleocapsid protein p7; by host PRMT6By similarity

Post-translational modificationi

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).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

Keywords - PTMi

Lipoprotein, Methylation, Myristate, Phosphoprotein

Interactioni

Subunit structurei

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).By similarity

Structurei

Secondary structure

1
501
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni178 – 1803Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1SJEX-ray2.45C167-182[»]
1SJHX-ray2.25C167-179[»]
3D3TX-ray2.80P446-455[»]
ProteinModelPortaliP12495.
SMRiP12495. Positions 2-434, 451-501.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP12495.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi16 – 227Nuclear export signalBy similarity
Motifi26 – 327Nuclear localization signalBy similarity
Motifi457 – 4604PTAP/PSAP motif
Motifi484 – 49310LYPX(n)L motif

Domaini

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).By similarity

Sequence similaritiesi

Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri392 – 40918CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri413 – 43018CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Family and domain databases

Gene3Di1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.
InterProiIPR000721. 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]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF08705. Gag_p6. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view]
PRINTSiPR00234. HIV1MATRIX.
SMARTiSM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEiPS50158. ZF_CCHC. 2 hits.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by ribosomal frameshifting. Align

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) [UniParc]FASTAAdd to Basket

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.

« Hide

        10         20         30         40         50
MGARASVLSG GKLDAWEKIR LRPGGKKKYR LKHLVWASRE LERFALNPGL
60 70 80 90 100
LETSDGCKQI IGQLQPAIRT GSEELRSLFN TVATLYCVHE RIEVKDTKEA
110 120 130 140 150
LEKMEEEQNK SKNKKAQQAA ADAGNNSQVS QNYPIVQNLQ GQMVHQAISP
160 170 180 190 200
RTLNAWVKVI EEKAFSPEVI PMFSALSEGA TPQDLNTMLN TVGGHQAAMQ
210 220 230 240 250
MLKETINEEA AEWDRLHPVH AGPIAPGQMR EPRGSDIAGT TSTLQEQIAW
260 270 280 290 300
MTSNPPIPVG EIYKRWIILG LNKIVRMYSP VSILDIRQGP KEPFRDYVDR
310 320 330 340 350
FYKTLRAEQA SQEVKGWMTE TLLVQNANPD CKTILKALGP QATLEEMMTA
360 370 380 390 400
CQGVGGPSHK ARVLAEAMSQ ATNSAAAVMM QRGNFKGPRK TIKCFNCGKE
410 420 430 440 450
GHIAKNCRAP RRKGCWKCGK EGHQLKDCTE RQANFLGKIW PSHKGRPGNF
460 470 480 490 500
LQSRPEPTAP PAESFGFGEE ITPSQKQEQK DKELYPSTAL KSLFGNDPLL

Q

Note: Produced by conventional translation.

Length:501
Mass (Da):55,678
Last modified:January 23, 2007 - v3
Checksum:i827C2609BC3E5963
GO
Isoform Gag-Pol polyprotein (identifier: P12499-1) [UniParc]FASTAAdd to Basket

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.

Length:1,436
Mass (Da):161,899
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M22639 Genomic RNA. Translation: AAA45365.1.
PIRiS54377.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M22639 Genomic RNA. Translation: AAA45365.1 .
PIRi S54377.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1SJE X-ray 2.45 C 167-182 [» ]
1SJH X-ray 2.25 C 167-179 [» ]
3D3T X-ray 2.80 P 446-455 [» ]
ProteinModelPortali P12495.
SMRi P12495. Positions 2-434, 451-501.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei P12495.

Family and domain databases

Gene3Di 1.10.1200.30. 1 hit.
1.10.150.90. 1 hit.
1.10.375.10. 1 hit.
4.10.60.10. 1 hit.
InterProi IPR000721. 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 ]
Pfami PF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 1 hit.
PF08705. Gag_p6. 1 hit.
PF00098. zf-CCHC. 2 hits.
[Graphical view ]
PRINTSi PR00234. HIV1MATRIX.
SMARTi SM00343. ZnF_C2HC. 2 hits.
[Graphical view ]
SUPFAMi SSF47353. SSF47353. 1 hit.
SSF47836. SSF47836. 1 hit.
SSF47943. SSF47943. 1 hit.
SSF57756. SSF57756. 1 hit.
PROSITEi PS50158. ZF_CCHC. 2 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiGAG_HV1Z2
AccessioniPrimary (citable) accession number: P12495
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 133 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

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).

Keywords - Technical termi

3D-structure

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3