2X83 | pdb_00002x83

Evolutionary basis of HIV restriction by the antiretroviral TRIMCyp

External Resource: Annotation

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: 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	8101425	3000745	SCOP2B (2022-06-29)
C	SCOP2 Family	Retrovirus capsid protein, N-terminal core domain	8101424	4001095	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Retrovirus capsid protein, N-terminal core domain	8101425	3000745	SCOP2 (2022-06-29)
B	SCOP2 Family	Cyclophilin peptidylprolyl isomerase-like	8065058	4000390	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Cyclophilin-like	8065059	3000168	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Cyclophilin-like	8065059	3000168	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_N	e2x83A1	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_N	e2x83C1	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	Pro_isomerase	e2x83B1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
D	Pro_isomerase	e2x83D1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	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)
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)
B	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	CATH (4.3.0)
D	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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
B, D	PF00160	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD (Pro_isomerase)	Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond pr ...	The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organisms studied so far and catalyse peptidyl-prolyl isomerisation during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilised in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	HIV-1 CAPSID	structural molecule activity RNA binding 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 cellular anatomical structure host cell part host intracellular region host cell nucleus host intracellular organelle viral nucleocapsid viral capsid virion component host cell cytoplasm
B, D	TRIM5/CypA fusion protein	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity amide binding binding cyclosporin A binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, C	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, C	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A, C	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, C	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, C	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, C	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
B, D	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
B, D	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
B, D	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
B, D	IPR000315	B-box-type zinc finger	Domain
B, D	IPR027370	Zinc finger, RING-type, eukaryotic	Domain
B, D	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B, D	IPR001841	Zinc finger, RING-type	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.