6SKN | pdb_00006skn

Structure of the native full-length HIV-1 capsid protein in helical assembly (-13,8)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
R	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
Q [auth P]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
P [auth N]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
O [auth L]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
N [auth J]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
M [auth H]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
L [auth Q]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
K [auth O]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
J [auth M]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077062	3001819	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
R	Glyco_hydro_42	e6sknR1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
Q [auth P]	Glyco_hydro_42	e6sknP1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
P [auth N]	Glyco_hydro_42	e6sknN1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
O [auth L]	Glyco_hydro_42	e6sknL1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
N [auth J]	Glyco_hydro_42	e6sknJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
M [auth H]	Glyco_hydro_42	e6sknH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
L [auth Q]	Glyco_hydro_42	e6sknQ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
K [auth O]	Glyco_hydro_42	e6sknO1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
J [auth M]	Glyco_hydro_42	e6sknM1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
I [auth K]	Glyco_hydro_42	e6sknK1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
H [auth I]	Glyco_hydro_42	e6sknI1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
G	Glyco_hydro_42	e6sknG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
F	Glyco_hydro_42	e6sknF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
E	Glyco_hydro_42	e6sknE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
D	Glyco_hydro_42	e6sknD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
C	Glyco_hydro_42	e6sknC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
B	Glyco_hydro_42	e6sknB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)
A	Glyco_hydro_42	e6sknA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_hydro_42	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	PF19317	Gag protein p24 C-terminal domain (Gag_p24_C)	Gag protein p24 C-terminal domain	p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	Gag protein	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding identical protein binding protein binding peptidase activity catalytic activity, acting on a protein integrase activity aspartic-type peptidase activity aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle symbiont entry into host cell symbiont entry into host viral genome integration into host DNA viral penetration into host nucleus symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction viral process viral life cycle symbiont entry into host cell symbiont entry into host viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process nucleobase-containing compound metabolic process DNA recombination DNA metabolic process nucleic acid metabolic process symbiont-mediated activation of host programmed cell death symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death disruption of cell in another organism symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing	host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane host cell virion membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR018061	Retropepsins	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR010659	Reverse transcriptase connection	Domain
A, B, C, D, E, A, B, C, D, E, F, G, H [auth I], I [auth K], J [auth M], K [auth O], L [auth Q], M [auth H], N [auth J], O [auth L], P [auth N], Q [auth P], R	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily