6Y9V

Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-8,13)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
F [auth H]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
H [auth N]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
J [auth d]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
K [auth e]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
L [auth j]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
M [auth k]	SCOP2B Superfamily	Retrovirus capsid dimerization domain-like	8077052	3001819	SCOP2B (2022-06-29)
G [auth J]	SCOP2B Superfamily	Cyclophilin-like	8043341	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	e6y9vA1	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	e6y9vB1	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	e6y9vB2	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	e6y9vC1	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	e6y9vC2	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	e6y9vD1	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	e6y9vD2	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 G]	Gag_p24_C	e6y9vG1	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 G]	Gag_p24_N	e6y9vG2	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 H]	Gag_p24_C	e6y9vH2	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 H]	Gag_p24_N	e6y9vH1	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 N]	Gag_p24_C	e6y9vN1	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 Y]	Gag_p24_N	e6y9vY1	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 d]	Gag_p24_C	e6y9vd2	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 d]	Gag_p24_N	e6y9vd1	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 e]	Gag_p24_C	e6y9ve2	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 e]	Gag_p24_N	e6y9ve1	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 j]	Gag_p24_C	e6y9vj1	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 k]	Gag_p24_C	e6y9vk2	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 k]	Gag_p24_N	e6y9vk1	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 J]	Pro_isomerase	e6y9vJ1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	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, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	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
G [auth J]	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, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	Gag-Pol 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 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 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 virion component virion membrane host cell nuclear membrane host cell membrane host cell nucleus host cell nuclear part host cell endomembrane system host cell nuclear envelope host cell plasma membrane viral nucleocapsid viral capsid
G [auth J]	Peptidyl-prolyl cis-trans isomerase A	isomerase activity RNA polymerase II CTD heptapeptide repeat modifying activity catalytic activity, acting on a protein RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity RNA polymerase II CTD heptapeptide repeat P6 isomerase activity peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity RNA polymerase II CTD heptapeptide repeat P3 isomerase activity amide binding binding cyclosporin A binding glycosaminoglycan binding organic acid binding isomerase activity RNA polymerase II CTD heptapeptide repeat modifying activity catalytic activity, acting on a protein RNA polymerase II CTD heptapeptide repeat peptidyl-prolyl isomerase activity RNA polymerase II CTD heptapeptide repeat P6 isomerase activity peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity RNA polymerase II CTD heptapeptide repeat P3 isomerase activity amide binding binding cyclosporin A binding glycosaminoglycan binding organic acid binding ion binding heparan sulfate binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding sulfur compound binding RNA binding nucleic acid binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding unfolded protein binding virion binding	cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade negative regulation of biological process regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade cellular response to stress cellular response to stimulus regulation of cellular process response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of stress-activated MAPK cascade negative regulation of biological process regulation of cellular response to stress regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication stress-activated MAPK cascade cellular response to stress regulation of intracellular signal transduction response to stress regulation of response to stress intracellular signaling cassette negative regulation of cellular process signal transduction regulation of biological process regulation of signaling negative regulation of response to stimulus biological regulation regulation of stress-activated protein kinase signaling cascade regulation of MAPK cascade negative regulation of signal transduction regulation of stress-activated MAPK cascade stress-activated protein kinase signaling cascade regulation of response to stimulus negative regulation of stress-activated protein kinase signaling cascade MAPK cascade regulation of cell communication cellular process negative regulation of MAPK cascade regulation of apoptotic process regulation of programmed cell death cell death apoptotic signaling pathway apoptotic process programmed cell death regulation of apoptotic signaling pathway protein folding biosynthetic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process activation of protein kinase B activity positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of cellular process protein phosphorylation positive regulation of transferase activity positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of catalytic activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of kinase activity activation of protein kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process regulation of metabolic process cell chemotaxis chemotaxis neutrophil chemotaxis response to external stimulus neutrophil migration granulocyte migration leukocyte migration cellular response to chemical stimulus taxis immune system process granulocyte chemotaxis response to chemical myeloid leukocyte migration cell migration cell motility leukocyte chemotaxis locomotion negative regulation of phosphate metabolic process negative regulation of protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of protein phosphorylation negative regulation of phosphorus metabolic process negative regulation of phosphorylation multicellular organismal process regulation of body fluid levels wound healing homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion coagulation regulation of biological quality response to wounding platelet activation response to oxidative stress cellular response to oxidative stress cellular response to chemical stress negative regulation of catalytic activity negative regulation of kinase activity negative regulation of transferase activity negative regulation of molecular function negative regulation of protein kinase activity negative regulation of viral process regulation of viral process regulation of viral life cycle negative regulation of viral life cycle viral process viral life cycle positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression regulation of DNA-binding transcription factor activity regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cellular component organization organelle organization lipid droplet organization cellular component organization or biogenesis positive regulation of viral genome replication positive regulation of viral process viral genome replication regulation of viral genome replication peptidyl-amino acid modification peptidyl-proline modification protein peptidyl-prolyl isomerization developmental process cellular developmental process nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development system development negative regulation of post-translational protein modification regulation of protein K48-linked ubiquitination regulation of protein ubiquitination protein ubiquitination regulation of protein modification by small protein conjugation or removal negative regulation of protein ubiquitination regulation of protein polyubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification protein polyubiquitination negative regulation of protein K48-linked ubiquitination negative regulation of protein polyubiquitination post-translational protein modification protein modification by small protein conjugation protein K48-linked ubiquitination protein modification by small protein conjugation or removal positive regulation of cell communication positive regulation of signal transduction positive regulation of response to stimulus positive regulation of MAPK cascade positive regulation of intracellular signal transduction positive regulation of signaling protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization transport positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport localization regulation of secretion by cell secretion by cell positive regulation of secretion cellular macromolecule localization regulation of transport secretion regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion establishment of localization positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport protein transport regulation of cellular localization macromolecule localization positive regulation of protein localization intrinsic apoptotic signaling pathway in response to oxidative stress regulation of oxidative stress-induced intrinsic apoptotic signaling pathway regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway intrinsic apoptotic signaling pathway negative regulation of programmed cell death negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway negative regulation of intrinsic apoptotic signaling pathway negative regulation of apoptotic process exit from host cell biological process involved in interspecies interaction between organisms viral release from host cell biological process involved in interaction with host biological process involved in symbiotic interaction cell adhesion molecule production endothelial cell activation	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol anchoring junction cell junction focal adhesion cell-substrate junction membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle protein-containing complex vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR014817	Gag protein p6	Domain
A, B, C, D, E [auth G], A, B, C, D, E [auth G], F [auth H], H [auth N], I [auth Y], J [auth d], K [auth e], L [auth j], M [auth k]	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily
G [auth J]	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
G [auth J]	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
G [auth J]	IPR024936	Cyclophilin-type peptidyl-prolyl cis-trans isomerase	Family
G [auth J]	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
G [auth J]	Pharos: P62937	squamous cell carcinoma non-small cell lung carcinoma Neoplasm Metastasis rheumatoid arthritis breast cancer gastric neoplasm mucocutaneous lymph node syndrome ovarian cancer peripheral nervous system disease schizophrenia dry eye syndrome hereditary diffuse gastric adenocarcinoma myopathy oral cavity neoplasm pancreatic intraductal papillary-mucinous carcinoma squamous cell carcinoma non-small cell lung carcinoma Neoplasm Metastasis rheumatoid arthritis breast cancer gastric neoplasm mucocutaneous lymph node syndrome ovarian cancer peripheral nervous system disease schizophrenia dry eye syndrome hereditary diffuse gastric adenocarcinoma myopathy oral cavity neoplasm pancreatic intraductal papillary-mucinous carcinoma peripheral neuropathy gastric cancer juvenile dermatomyositis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia