5MD9 | pdb_00005md9

The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=17, twist=6

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
N [auth J]	Gag_p24_N	e5md9J1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
M [auth I]	Gag_p24_N	e5md9I1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
L [auth H]	Gag_p24_N	e5md9H1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
G [auth f]	Gag_p24_N	e5md9f1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
F [auth b]	Gag_p24_N	e5md9b1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
E [auth a]	Gag_p24_N	e5md9a1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_p24_N	ECOD (1.6)
K [auth G]	Gag_p24_C	e5md9G1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
J [auth E]	Gag_p24_C	e5md9E1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
I [auth D]	Gag_p24_C	e5md9D1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
H [auth C]	Gag_p24_C	e5md9C1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
D [auth W]	Gag_p24_C	e5md9W1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
C [auth F]	Gag_p24_C	e5md9F1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
B	Gag_p24_C	e5md9B1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)
A	Gag_p24_C	e5md9A1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_p24_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	PF00607	gag protein p24 N-terminal domain (Gag_p24)	gag protein p24 N-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
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	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
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	Capsid protein p24 N-terminal domain	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation virion assembly viral budding viral budding via host ESCRT complex viral life cycle	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 membrane 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 membrane virion component virion membrane host cell nucleus host cell plasma membrane host cell membrane viral nucleocapsid viral capsid
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	Capsid protein p24 C-terminal domain	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation virion assembly viral budding viral budding via host ESCRT complex viral life cycle	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 membrane 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 membrane virion component virion membrane host cell nucleus host cell plasma membrane host cell membrane viral nucleocapsid viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR001878	Zinc finger, CCHC-type	Domain
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR010999	Retroviral matrix protein	Homologous Superfamily
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR014817	Gag protein p6	Domain
E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], E [auth a], F [auth b], G [auth f], L [auth H], M [auth I], N [auth J]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR014817	Gag protein p6	Domain
A, B, C [auth F], D [auth W], H [auth C], A, B, C [auth F], D [auth W], H [auth C], I [auth D], J [auth E], K [auth G]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily