5UP4 | pdb_00005up4

Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
R [auth J]	ATP-synt_Eps	e5up4J1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
Q [auth I]	ATP-synt_Eps	e5up4I1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
P [auth H]	ATP-synt_Eps	e5up4H1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
O [auth G]	ATP-synt_Eps	e5up4G1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
N [auth F]	ATP-synt_Eps	e5up4F1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
M [auth E]	ATP-synt_Eps	e5up4E1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
L [auth D]	ATP-synt_Eps	e5up4D1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
K [auth C]	ATP-synt_Eps	e5up4C1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
J [auth S]	ATP-synt_Eps	e5up4S1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
I [auth R]	ATP-synt_Eps	e5up4R1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
H [auth Q]	ATP-synt_Eps	e5up4Q1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
G [auth P]	ATP-synt_Eps	e5up4P1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
F [auth O]	ATP-synt_Eps	e5up4O1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
E [auth N]	ATP-synt_Eps	e5up4N1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
D [auth M]	ATP-synt_Eps	e5up4M1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
C [auth L]	ATP-synt_Eps	e5up4L1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
B [auth K]	ATP-synt_Eps	e5up4K1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: ATP-synt_Eps	ECOD (v294.1)
A [auth B]		e5up4B1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Undecaprenyl diphosphate synthase	F:	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	HIV-1 Capsid Protein and spacer peptide 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding structural molecule activity cation binding transition metal ion binding zinc ion binding metal ion binding RNA binding nucleic acid binding	viral gene expression viral process viral translational frameshifting viral translation	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 [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR001878	Zinc finger, CCHC-type	Domain
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR010999	Retroviral matrix protein	Homologous Superfamily
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	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.