Annotations: 3J4F

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8036123	3000745	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)
A	Gag_p24_C	e3j4fA2	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_N	e3j4fA1	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)
B	Gag_p24_C	e3j4fB2	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_N	e3j4fB1	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)
C	Gag_p24_C	e3j4fC2	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	Gag_p24_N	e3j4fC1	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)
D	Gag_p24_C	e3j4fD2	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	Gag_p24_N	e3j4fD1	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	Gag_p24_C	e3j4fE2	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)
E	Gag_p24_N	e3j4fE1	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	Gag_p24_C	e3j4fF2	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	Gag_p24_N	e3j4fF1	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, D, E A, B, C, D, E, F	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, D, E A, B, C, D, E, F	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	capsid protein	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 identical protein binding protein 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 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 host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body 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
A, B, C, D, E A, B, C, D, E, F	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR014817	Gag protein p6	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.