Molecular Target Synopsis
Domains and Structures
Drugs and Clinical Candidates
Ligand Efficiency Plot
Family Cladogram
Interaction Network
Gene Expression
Gene Copy Number Variation
Germline Genetics

gag-pol (P03366) - Overview - Molecular Target Synopsis


gag-pol, Gag-Pol polyprotein
Enzyme Classification
UniProt P03366

Also Known as POL_HV1B1, gag-pol

Gag-Pol polyprotein: Mediates, with Gag polyprotein, 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). Gag-Pol polyprotein may regulate its own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, the polyprotein would promote translation, whereas at high concentration, the polyprotein would encapsidate genomic RNA and then shut off translation., Matrix protein p17: Targets the polyprotein to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. Matrix protein is part of the pre-integration complex. Implicated in the release from host cell mediated by Vpu. Binds to RNA., 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. On the other hand, interactions with PDZD8 or CYPA stabilize the capsid., 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 in gRNA dimerization, packaging, tRNA incorporation and virion assembly., Protease: Aspartyl protease that 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. Hydrolyzes host EIF4GI and PABP1 in order to shut off the capped cellular mRNA translation. The resulting inhibition of cellular protein synthesis serves to ensure maximal viral gene expression and to evade host immune response (By similarity)., Reverse transcriptase/ribonuclease H: 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 o Matrix protein p17: Homotrimer; further assembles as hexamers of trimers (By similarity). Matrix protein p17: Interacts with gp41 (via C-terminus) (By similarity). Matrix protein p17: interacts with host CALM1; this interaction induces a conformational change in the Matrix protein, triggering exposure of the myristate group (By similarity). Matrix protein p17: interacts with host AP3D1; this interaction allows the polyprotein trafficking to multivesicular bodies during virus assembly (By similarity). Matrix protein p17: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase (By similarity). Capsid protein p24: Homodimer; the homodimer further multimerizes as homohexamers or homopentamers. Capsid protein p24: Interacts with human PPIA/CYPA (By similarity); This interaction stabilizes the capsid. Capsid protein p24: Interacts with human NUP153 (By similarity). Capsid protein p24: Interacts with host PDZD8; this interaction stabilizes the capsid (By similarity). Capsid protein p24: Interacts with monkey TRIM5; this interaction destabilizes the capsid (By similarity).Protease: Homodimer, whose active site consists of two apposed aspartic acid residues. Reverse transcriptase/ribonuclease H: 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: Homodimer; possibly can form homotetramer. Integrase: Part of the pre-integration complex (PIC) which is composed of viral genome, matrix protein, Vpr and integrase. Integrase: Interacts with human SMARCB1/INI1 and human PSIP1/LEDGF isoform 1. Integrase: Interacts with human KPNA3; this interaction might play a role in nuclear import of the pre-integration complex (By similarity). Integrase: Interacts with human NUP153; this interaction might play a role in nuclear import of the pre-integration complex (By similarity).

Inspect Structure
See all 3D Structures for gag-pol

Isoforms / Transcripts (Protein Coding)

Protein Length Ensembl Gene Ensembl Transcript Ensembl Protein Uniprot Isoform


gag-pol is targeted by Approved Drugs Zidovudine, Tenofovir Disoproxil, Nevirapine, Efavirenz, Abacavir, Zalcitabine. (see details)
Tenofovir Disoproxil

Sub-cellular localization

UniProt: gag-pol is active in the following subcellular-locations: host cell membrane, host cytoplasm, host endosome, host multivesicular body, host nucleus, virion, virion membrane.
GO terms: gag-pol is active in the following subcellular-locations: host cell nucleus, host cell plasma membrane, host multivesicular body, viral nucleocapsid, virion membrane.

GO terms

Gene Copy Number Variation

In COSMIC - Cell Lines Project gag-pol has gain in 0 cell-lines, loss in 0 cell-lines and no signal in 0 cell-lines. (see details)

3D Structures

For gag-pol there are:
300 structures (688 chains) solved
259 are solved in complex with at least one small molecule ligand
52 are solved with an approved drug

gag-pol is solved in complex with the approved drug(s):

SUC/SUCROSE (2BE2_A, 2BE2_B, 2I5J_A, 4R5P_B, 4R5P_D, 5D3G_B, 5D3G_D, 5HLF_B, 5HLF_D, 5HP1_B, 5HP1_D, 5HRO_B, 5HRO_D, 5I3U_B, 5I3U_D, 5TXL_B, 5TXL_D, 5TXM_B, 5TXM_D, 5TXN_B, 5TXN_D, 5TXO_B, 5TXO_D, 5TXP_B, 5TXP_D, 6BHJ_B, 6BHJ_D, 6HAK_B),
NVP/NEVIRAPINE (3HVT_A, 3V81_A, 3V81_C, 4PUO_A, 4PUO_C, 4PWD_A, 4PWD_C, 4Q0B_A, 4Q0B_C, 5HBM_A),
T27/RILPIVIRINE (2ZD1_A, 2ZE2_A, 3BGR_A, 3QLH_A, 4G1Q_A, 4ICL_A, 4ID5_A, 4IDK_A, 4IFV_A, 4IFY_A, 4IG3_A, 4KFB_A, 5CYM_A, 5CYQ_A, 6ELI_A),
478/AMPRENAVIR (3NU3_B, 3NU4_B, 3NU5_B, 3NU6_B, 3NU9_A, 3NUJ_B, 3NUO_B),

(see details)
Molecular Target 3D Synopsis

Screening and Chemistry

gag-pol has been screened with 8 compounds (8 bioactivities). (see details)