4LQW | pdb_00004lqw

Crystal structure of HIV-1 capsid N-terminal domain in complex with NUP358 cyclophilin

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4lqwd_	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 type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ],	SCOPe (2.08)
C	d4lqwc_	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 type 1 (NEW YORK-5 ISOLATE) ) [TaxId: 11698 ],	SCOPe (2.08)
B	d4lqwb1	All beta proteins	Cyclophilin-like	Cyclophilin-like	Cyclophilin (peptidylprolyl isomerase)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4lqwb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4lqwa1	All beta proteins	Cyclophilin-like	Cyclophilin-like	Cyclophilin (peptidylprolyl isomerase)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4lqwa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Cyclophilin-like	8065071	3000168	SCOP2B (2022-06-29)
A	SCOP2 Family	Cyclophilin peptidylprolyl isomerase-like	8065070	4000390	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cyclophilin-like	8065071	3000168	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	e4lqwD1	A: PRTase-like	X: PRTase-like	H: PRTase-like	T: Pribosyltran	F:	ECOD (20:10:01)
C	e4lqwC1	A: immunoglobulin/albumin-binding domain-like	X: EGF-related	H: Complement control module/SCR domain	T: Asp	F:	ECOD (20:10:01)
B	e4lqwB1	A: PRTase-like	X: PRTase-like	H: PRTase-like	T: Pribosyltran	F:	ECOD (20:10:01)
A	e4lqwA1	A: immunoglobulin/albumin-binding domain-like	X: EGF-related	H: Complement control module/SCR domain	T: Asp	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
A	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, 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
C, D	Capsid protein p24	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 hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity 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 hydrolase activity, acting on ester bonds nuclease activity 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 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, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression 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 symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression 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 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 regulation of killing of cells of another organism disruption of cell in another organism regulation of cell killing symbiont-mediated perturbation of host apoptosis disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing proteolysis protein metabolic process	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 viral nucleocapsid 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 viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane host cell virion membrane host cell nucleus
A, B	E3 SUMO-protein ligase RanBP2	small GTPase binding protein binding binding enzyme binding GTPase binding RNA binding nucleic acid binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity protein-macromolecule adaptor activity small GTPase binding protein binding binding enzyme binding GTPase binding RNA binding nucleic acid binding enzyme regulator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity kinase regulator activity protein-macromolecule adaptor activity molecular adaptor activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity protein-containing complex binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process biosynthetic process regulation of gluconeogenesis metabolic process cellular process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process cellular homeostasis chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis intracellular chemical homeostasis intracellular glucose homeostasis localization centrosome localization microtubule organizing center localization RNA transport nitrogen compound transport transport nucleic acid transport mRNA transport establishment of localization establishment of RNA localization macromolecule localization RNA localization nucleobase-containing compound transport protein folding protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation cellular localization nucleocytoplasmic transport nuclear transport establishment of localization in cell intracellular transport peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal nuclear export establishment of protein localization NLS-bearing protein import into nucleus protein localization to nucleus import into nucleus establishment of protein localization to organelle protein transport protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport response to amine response to stimulus response to chemical response to nitrogen compound response to amphetamine negative regulation of biological process RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane organelle membrane cytoplasmic periphery of the nuclear pore complex cellular anatomical structure membrane membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system nuclear membrane organelle membrane cytoplasmic periphery of the nuclear pore complex perinuclear region of cytoplasm cytoplasm cytosol protein-containing complex nuclear protein-containing complex nuclear pore membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen nuclear pore nuclear basket catalytic complex SUMO ligase complex transferase complex inclusion body nuclear inclusion body nuclear outer membrane-endoplasmic reticulum membrane network annulate lamellae nuclear pore cytoplasmic filaments

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
A, B	IPR022011	Nup358/RanBP2 E3 ligase domain	Domain
A, B	IPR029000	Cyclophilin-like domain superfamily	Homologous Superfamily
A, B	IPR002130	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain	Domain
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR019734	Tetratricopeptide repeat	Repeat
A, B	IPR020892	Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site	Conserved Site
A, B	IPR036443	Zinc finger, RanBP2-type superfamily	Homologous Superfamily
A, B	IPR000156	Ran binding domain	Domain
A, B	IPR001876	Zinc finger, RanBP2-type	Domain
A, B	IPR045255	Ran binding protein RanBP1-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P49792	familial acute necrotizing encephalopathy inflammatory myofibroblastic tumor psoriasis acute necrotizing encephalitis breast carcinoma ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive hereditary spastic paraplegia lung cancer ovarian cancer tuberculosis adrenal cortex carcinoma dermatomyositis ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED, SUSCEPTIBILITY TO, 3 glioblastoma hypohidrotic ectodermal dysplasia familial acute necrotizing encephalopathy inflammatory myofibroblastic tumor psoriasis acute necrotizing encephalitis breast carcinoma ectodermal dysplasia 10B, hypohidrotic/hair/tooth type, autosomal recessive hereditary spastic paraplegia lung cancer ovarian cancer tuberculosis adrenal cortex carcinoma dermatomyositis ENCEPHALOPATHY, ACUTE, INFECTION-INDUCED, SUSCEPTIBILITY TO, 3 glioblastoma hypohidrotic ectodermal dysplasia malignant mesothelioma plasma cell myeloma atypical teratoid rhabdoid tumor ectodermal dysplasia 10A, hypohidrotic/hair/nail type, autosomal dominant myopathy