4DGA

TRIMCyp cyclophilin domain from Macaca mulatta: HIV-1 CA(O-loop) complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4dgaa_	All beta proteins	Cyclophilin-like	Cyclophilin-like	Cyclophilin (peptidylprolyl isomerase)	automated matches	rhesus macaque (Macaca mulatta ) [TaxId: 9544 ],	SCOPe (2.08)
B	d4dgab_	All beta proteins	Cyclophilin-like	Cyclophilin-like	Cyclophilin (peptidylprolyl isomerase)	automated matches	rhesus macaque (Macaca mulatta ) [TaxId: 9544 ],	SCOPe (2.08)
C	d4dgac_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	HIV-1 capsid protein	HIV-1 (Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)
D	d4dgad_	All alpha proteins	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	Retrovirus capsid protein, N-terminal core domain	HIV-1 capsid protein	HIV-1 (Human immunodeficiency virus 1 ) [TaxId: 11676 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cyclophilin-like	8098874	3000168	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cyclophilin-like	8098874	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	Pro_isomerase	e4dgaA1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
B	Pro_isomerase	e4dgaB1	A: beta barrels	X: Cyclophilin-like (From Topology)	H: Cyclophilin-like (From Topology)	T: Cyclophilin-like	F: Pro_isomerase	ECOD (1.6)
C	Gag_p24_N	e4dgaC1	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_N	e4dgaD1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	CATH (4.3.0)
B	2.40.100.10	Mainly Beta	Beta Barrel	Cyclophilin	Cyclophilin-like	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)
D	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	TRIMCyp	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity glycosaminoglycan binding organic acid binding binding ion binding heparan sulfate binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity glycosaminoglycan binding organic acid binding binding ion binding heparan sulfate binding anion binding carboxylic acid binding carbohydrate derivative binding small molecule binding sulfur compound binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding amide binding cyclosporin A 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 peptidyl-amino acid modification peptidyl-proline modification protein peptidyl-prolyl isomerization 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 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 K48-linked ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal 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 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 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 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 regulation of viral life cycle regulation of viral process viral genome replication viral process regulation of viral genome replication viral life cycle cell adhesion molecule production endothelial cell activation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol extracellular region membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
C, D	capsid protein	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process symbiont entry into host viral life cycle viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell viral process symbiont entry into host viral life cycle viral genome integration into host DNA viral penetration into host nucleus intracellular transport of virus transport of virus nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation DNA recombination regulation of biological process symbiont-mediated perturbation of host cellular process symbiont-mediated activation of host programmed cell death regulation of cellular process symbiont-mediated activation of host apoptosis symbiont-mediated perturbation of host programmed cell death biological regulation disruption of cell in another organism regulation of killing of cells of another organism regulation of cell killing disruption of anatomical structure in another organism symbiont-mediated perturbation of host apoptosis symbiont-mediated killing of host cell killing of cells of another organism cell killing proteolysis protein metabolic process	cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid cellular anatomical structure membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane host cell virion membrane host cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
A, B	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
A, B	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site
A, B	IPR024936	Cyclophilin-type peptidyl-prolyl cis-trans isomerase	Family
C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C, D	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
C, D	IPR001878	Zinc finger, CCHC-type	Domain
C, D	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
C, D	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
C, D	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
C, D	IPR018061	Retropepsins	Domain
C, D	IPR010661	Reverse transcriptase thumb	Domain
C, D	IPR002156	Ribonuclease H domain	Domain
C, D	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
C, D	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
C, D	IPR001584	Integrase, catalytic core	Domain
C, D	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
C, D	IPR010999	Retroviral matrix protein	Homologous Superfamily
C, D	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
C, D	IPR001969	Aspartic peptidase, active site	Active Site
C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C, D	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
C, D	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C, D	IPR001037	Integrase, C-terminal, retroviral	Domain
C, D	IPR034170	Retropepsin-like catalytic domain	Domain
C, D	IPR000477	Reverse transcriptase domain	Domain
C, D	IPR010659	Reverse transcriptase connection	Domain
C, D	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily