5UP4 | pdb_00005up4

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

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)
R [auth J]	Gag_p24_C	e5up4J1	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)
R [auth J]	Gag_p24_N	e5up4J2	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)
Q [auth I]	Gag_p24_C	e5up4I1	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)
Q [auth I]	Gag_p24_N	e5up4I2	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)
P [auth H]	Gag_p24_C	e5up4H2	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)
P [auth H]	Gag_p24_N	e5up4H1	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)
O [auth G]	Gag_p24_C	e5up4G2	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)
O [auth G]	Gag_p24_N	e5up4G1	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 F]	Gag_p24_C	e5up4F2	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)
N [auth F]	Gag_p24_N	e5up4F1	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 E]	Gag_p24_C	e5up4E1	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)
M [auth E]	Gag_p24_N	e5up4E2	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 D]	Gag_p24_C	e5up4D1	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)
L [auth D]	Gag_p24_N	e5up4D2	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)
K [auth C]	Gag_p24_C	e5up4C2	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 C]	Gag_p24_N	e5up4C1	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)
J [auth S]	Gag_p24_C	e5up4S2	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 S]	Gag_p24_N	e5up4S1	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)
I [auth R]	Gag_p24_C	e5up4R2	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 R]	Gag_p24_N	e5up4R1	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)
H [auth Q]	Gag_p24_C	e5up4Q2	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 Q]	Gag_p24_N	e5up4Q1	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 P]	Gag_p24_C	e5up4P2	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)
G [auth P]	Gag_p24_N	e5up4P1	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 [auth O]	Gag_p24_C	e5up4O1	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 O]	Gag_p24_N	e5up4O2	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 N]	Gag_p24_C	e5up4N2	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 [auth N]	Gag_p24_N	e5up4N1	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 [auth M]	Gag_p24_C	e5up4M2	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 M]	Gag_p24_N	e5up4M1	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 [auth L]	Gag_p24_C	e5up4L1	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 L]	Gag_p24_N	e5up4L2	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 [auth K]	Gag_p24_C	e5up4K2	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 [auth K]	Gag_p24_N	e5up4K1	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 [auth B]	Gag_p24_C	e5up4B1	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 [auth B]	Gag_p24_N	e5up4B2	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 [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]	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 [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]	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 [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 membrane 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 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 [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