5MDF

The structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=23, 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)
B	Gag_p24_C	e5mdfB1	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	e5mdfF1	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	e5mdfW1	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	e5mdfC1	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	e5mdfE1	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)
K [auth G]	Gag_p24_C	e5mdfG1	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	e5mdfA1	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	e5mdfD1	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)
F [auth b]	Gag_p24_N	e5mdfb1	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	e5mdfI1	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)
N [auth J]	Gag_p24_N	e5mdfJ1	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	e5mdfa1	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	e5mdff1	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	e5mdfH1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
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]	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 [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]	Gag protein	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding organic cyclic compound binding nucleic acid binding	virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle	virion component virion membrane viral nucleocapsid viral capsid intracellular anatomical structure cytoplasm cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region
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]	Gag protein	structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding organic cyclic compound binding nucleic acid binding	virion assembly viral process viral budding viral budding via host ESCRT complex viral life cycle	virion component virion membrane viral nucleocapsid viral capsid intracellular anatomical structure cytoplasm cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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]	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
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]	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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.