5UPW | pdb_00005upw

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
F	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	3001819	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077054	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)
F	Gag_p24_C	e5upwF2	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	e5upwF1	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	e5upwE2	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	e5upwE1	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	e5upwD1	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	e5upwD2	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	e5upwC2	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	e5upwC1	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	e5upwB1	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	e5upwB2	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)
A	Gag_p24_C	e5upwA2	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	e5upwA1	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)

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 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 virion component 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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.