1U7K | pdb_00001u7k

Structure of a hexameric N-terminal domain from murine leukemia virus capsid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1u7ka_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)
B	d1u7kb_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)
C	d1u7kc_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)
D	d1u7kd_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)
E	d1u7ke_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)
F	d1u7kf_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	AKV capsid	(AKR (endogenous) murine leukemia virus ) [TaxId: 11791 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Retrovirus capsid protein, N-terminal core domain	8030423	4001095	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	3000745	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	3000745	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	3000745	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	3000745	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	3000745	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Retrovirus capsid protein, N-terminal core domain	8042802	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_p30	e1u7kA1	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_p30	ECOD (1.6)
B	Gag_p30	e1u7kB1	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_p30	ECOD (1.6)
C	Gag_p30	e1u7kC1	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_p30	ECOD (1.6)
D	Gag_p30	e1u7kD1	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_p30	ECOD (1.6)
E	Gag_p30	e1u7kE1	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_p30	ECOD (1.6)
F	Gag_p30	e1u7kF1	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_p30	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
B	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
C	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
D	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
E	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)
F	1.10.375.10	Mainly Alpha	Orthogonal Bundle	Human Immunodeficiency Virus Type 1 Capsid Protein	Human Immunodeficiency Virus Type 1 Capsid Protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF02093	Gag P30 core shell protein (Gag_p30)	Gag P30 core shell protein	-	Family

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	Gag polyprotein	structural constituent of virion 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	virion assembly viral process 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 host cell plasma membrane 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 host cell plasma membrane host cell membrane viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR050462	Retroviral Gag-Pol polyproteins	Family
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	IPR000840	Gamma-retroviral matrix protein	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	IPR036946	Gamma-retroviral matrix domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR002079	Gag polyprotein, inner coat protein p12	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003036	Core shell protein Gag P30	Domain

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.