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Protein

Gag polyprotein

Gene

gag

Organism
Human immunodeficiency virus type 2 subtype A (isolate Ghana-1) (HIV-2)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Gag polyprotein: Mediates, with Gag-Pol polyrotein, the essential events in virion assembly, including binding the plasma membrane, making the protein-protein interactions necessary to create spherical particles, recruiting the viral Env proteins, and packaging the genomic RNA via direct interactions with the RNA packaging sequence (Psi).By similarity
Matrix protein p17: Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus (By similarity). Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA (By similarity).By similarity
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 disassembled soon after virion entry (By similarity). Host restriction factors such as TRIM5-alpha or TRIMCyp bind retroviral capsids and cause premature capsid disassembly, leading to blocks in reverse transcription. Capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species. Host PIN1 apparently facilitates the virion uncoating (By similarity). On the other hand, interactions with PDZD8 or CYPA stabilize the capsid (By similarity).By similarity
Nucleocapsid protein p7: Encapsulates and protects viral dimeric unspliced genomic RNA (gRNA). Binds these RNAs through its zinc fingers. Acts as a nucleic acid chaperone which is involved in rearangement of nucleic acid secondary structure during gRNA retrotranscription. Also facilitates template switch leading to recombination. As part of the polyprotein, participates to gRNA dimerization, packaging, tRNA incorporation and virion assembly.By similarity
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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri390 – 40718CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri411 – 42818CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

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:
Matrix protein p17
Short name:
MA
Capsid protein p24
Short name:
CA
Spacer peptide 1By similarity
Short name:
SP1
Alternative name(s):
p2
Spacer peptide 2By similarity
Short name:
SP2
Alternative name(s):
p1
Gene namesi
Name:gag
OrganismiHuman immunodeficiency virus type 2 subtype A (isolate Ghana-1) (HIV-2)
Taxonomic identifieri11717 [NCBI]
Taxonomic lineageiVirusesRetro-transcribing virusesRetroviridaeOrthoretrovirinaeLentivirusPrimate lentivirus group
Virus hostiHomo sapiens (Human) [TaxID: 9606]
Proteomesi
  • UP000007424 Componenti: Genome

Subcellular locationi

Gag polyprotein :
  • Host cell membrane By similarity; Lipid-anchor By similarity
  • Host endosomehost multivesicular body By similarity

  • Note: These locations are probably linked to virus assembly sites. The main location is the cell membrane, but under some circumstances, late endosomal compartments can serve as productive sites for virion assembly.By similarity
Matrix protein p17 :
  • Virion membrane By similarity; Lipid-anchor By similarity
  • Host nucleus By similarity
  • Host cytoplasm By similarity
Capsid protein p24 :
  • Virion By similarity
Nucleocapsid protein p7 :
  • Virion By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

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

Pathology & Biotechi

Keywords - Diseasei

AIDS

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved; by hostBy similarity
Chaini2 – 522521Gag polyproteinPRO_0000261245Add
BLAST
Chaini2 – 135134Matrix protein p17By similarityPRO_0000038607Add
BLAST
Chaini136 – 366231Capsid protein p24By similarityPRO_0000038608Add
BLAST
Peptidei367 – 38317Spacer peptide 1By similarityPRO_0000042075Add
BLAST
Chaini384 – 43249Nucleocapsid protein p7By similarityPRO_0000042076Add
BLAST
Peptidei433 – 44614Spacer peptide 2By similarityPRO_0000042077Add
BLAST
Chaini447 – 52276p6-gagBy similarityPRO_0000042078Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Lipidationi2 – 21N-myristoyl glycine; by hostBy similarity
Modified residuei151 – 1511Phosphoserine; by host MAPK1By similarity

Post-translational modificationi

Gag-Pol polyprotein: Specific enzymatic cleavages by the viral protease yield mature proteins.By similarity
Matrix protein p17: Tyrosine phosphorylated presumably in the virion by a host kinase. Phosphorylation is apparently not a major regulator of membrane association.By similarity
Capsid protein p24 is phosphorylated possibly by host MAPK1; this phosphorylation is necessary for Pin1-mediated virion uncoating.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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei135 – 1362Cleavage; by viral proteaseBy similarity
Sitei366 – 3672Cleavage; by viral proteaseBy similarity
Sitei383 – 3842Cleavage; by viral proteaseBy similarity
Sitei432 – 4332Cleavage; by viral proteaseBy similarity
Sitei446 – 4472Cleavage; by viral proteaseBy similarity

Keywords - PTMi

Lipoprotein, Myristate, Phosphoprotein

Interactioni

Subunit structurei

Gag polyprotein: Homotrimer; further assembles as hexamers of trimers. Oligomerization possibly creates a central hole into which the cytoplasmic tail of the gp41 envelope protein may be inserted.Gag polyprotein: Interacts with host TRIM22; this interaction seems to disrupt proper trafficking of Gag polyprotein and may interfere with budding. Gag polyprotein: Interacts with host PDZD8. Matrix protein p17: Homotrimer; further assembles as hexamers of trimers. Matrix protein p17: Interacts with gp41 (via C-terminus). Matrix protein p17: Interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group. Matrix protein p17: Interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly. Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA. Capsid protein p24: Interacts with human NUP153. Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid. Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid. p6-gag interacts with Vpr; this interaction allows Vpr incorporation into the virion. p6-gag interacts with host TSG101. p6-gag interacts with host PDCD6IP/AIP1.By similarity

Structurei

Secondary structure

1
522
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi386 – 3883Combined sources
Turni392 – 3954Combined sources
Helixi402 – 4043Combined sources
Beta strandi414 – 4163Combined sources
Helixi423 – 4253Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NC8NMR-A384-412[»]
2DI2NMR-A384-412[»]
2EC7NMR-A384-432[»]
ProteinModelPortaliP18041.
SMRiP18041. Positions 2-135, 146-381, 384-432.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP18041.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni7 – 3125Interaction with Gp41By similarityAdd
BLAST
Regioni8 – 4336Interaction with host CALM1By similarityAdd
BLAST
Regioni12 – 198Interaction with host AP3D1By similarity
Regioni14 – 3320Interaction with membrane phosphatidylinositol 4,5-bisphosphate and RNABy similarityAdd
BLAST
Regioni73 – 775Interaction with membrane phosphatidylinositol 4,5-bisphosphateBy similarity
Regioni192 – 22938Interaction with host PPIA/CYPA and NUP153By similarityAdd
BLAST
Regioni220 – 2278PPIA/CYPA-binding loopBy similarity
Regioni280 – 36687Dimerization/Multimerization of capsid protein p24By similarityAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi16 – 227Nuclear export signalBy similarity
Motifi26 – 327Nuclear localization signalBy similarity
Motifi457 – 4604PTAP/PSAP 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 one L domains: a PTAP/PSAP motif, which interacts with the UEV domain of TSG101 (By similarity).By similarity

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri390 – 40718CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri411 – 42818CCHC-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.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_HIV/RSV.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 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. AlignAdd to basket

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: P18041-1) [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
MGARNSVLRG KKADELEKIR LRPSGKKKYR LKHIVWAANE LDKFGLAESL
60 70 80 90 100
LESKEGCQKI LTVLDPLVPT GSENLKSLFN TVCVIWCLHA EEKVKDTEEA
110 120 130 140 150
KKLVQRHLGA ETGTAEKMPS TSRPTAPPSG RGRNFPVQQT GGGNYIHVPL
160 170 180 190 200
SPRTLNAWVK LVEDKKFGAE VVPGFQALSE GCTPYDINQM LNCVGDHQAA
210 220 230 240 250
MQIIREIIND EAADWDAQHP IPGPLPAGQL RDPRGSDIAG TTSTVEEQIQ
260 270 280 290 300
WMYRPQNPVP VGNIYRRWIQ IGLQKCVRMY NPTNILDVKQ GPKEPFQSYV
310 320 330 340 350
DRFYKSLRAE QTDPAVKNWM TQTLLIQNAN PDCKLVLKGL GMNPTLEEML
360 370 380 390 400
TACQGVGGPG QKARLMAEAL KEALTPPPIP FAAAQQRKVI RCWNCGKEGH
410 420 430 440 450
SARQCRAPRR QGCWKCGKTG HVMAKCPERQ AGFLGMGPWG KKPRNFPVAQ
460 470 480 490 500
APPGLIPTAP PADPAVDLLE RYMQQGREQR EQRERPYKEV TEDLLHLEQG
510 520
KAPHREATED LLHLNSLFGK DQ
Note: Produced by conventional translation.
Length:522
Mass (Da):58,206
Last modified:January 23, 2007 - v3
Checksum:i401341167A700553
GO
Isoform Gag-Pol polyprotein (identifier: P18042-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry P18042.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced by -1 ribosomal frameshifting.
Length:1,464
Mass (Da):164,882
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30895 Genomic DNA. Translation: AAA43932.1.
PIRiJS0327. FOLJGG.

Keywords - Coding sequence diversityi

Ribosomal frameshifting

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M30895 Genomic DNA. Translation: AAA43932.1.
PIRiJS0327. FOLJGG.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1NC8NMR-A384-412[»]
2DI2NMR-A384-412[»]
2EC7NMR-A384-432[»]
ProteinModelPortaliP18041.
SMRiP18041. Positions 2-135, 146-381, 384-432.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiP18041.

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.
IPR000071. Lentvrl_matrix_N.
IPR012344. Matrix_HIV/RSV.
IPR008916. Retrov_capsid_C.
IPR008919. Retrov_capsid_N.
IPR010999. Retrovr_matrix.
IPR001878. Znf_CCHC.
[Graphical view]
PfamiPF00540. Gag_p17. 1 hit.
PF00607. Gag_p24. 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]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiGAG_HV2G1
AccessioniPrimary (citable) accession number: P18041
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1990
Last sequence update: January 23, 2007
Last modified: October 14, 2015
This is version 118 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.