3NXD | pdb_00003nxd

JC polyomavirus VP1 in complex with LSTc

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
E	d3nxde_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	JCPyV (JC polyomavirus ) [TaxId: 10632 ],	SCOPe (2.08)
D	d3nxdd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	JCPyV (JC polyomavirus ) [TaxId: 10632 ],	SCOPe (2.08)
C [auth A]	d3nxda_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	JCPyV (JC polyomavirus ) [TaxId: 10632 ],	SCOPe (2.08)
B	d3nxdb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	JCPyV (JC polyomavirus ) [TaxId: 10632 ],	SCOPe (2.08)
A [auth C]	d3nxdc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	JCPyV (JC polyomavirus ) [TaxId: 10632 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Group I dsDNA viruses	8081603	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8081603	3000939	SCOP2B (2022-06-29)
C [auth A]	SCOP2 Family	papovaviridae-like vp	8081602	4003485	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Group I dsDNA viruses	8081603	3000939	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8081603	3000939	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Group I dsDNA viruses	8081603	3000939	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)
E	Phospholip_A2_1	e3nxdE1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
D	Phospholip_A2_1	e3nxdD1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
C [auth A]	Phospholip_A2_1	e3nxdA1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
B	Phospholip_A2_1	e3nxdB1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Phospholip_A2_1	ECOD (develop294)
A [auth C]	Glyco_hydro_66	e3nxdC1	A: alpha bundles	X: Lipocalins/Streptavidin	H: SAM/DNA-glycosylase	T: SAM domain-like	F: Glyco_hydro_66	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
D	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
C [auth A]	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
B	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
A [auth C]	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B, C [auth A], D, E	Major capsid protein VP1	structural molecule activity	import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis viral process symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host	viral capsid icosahedral viral capsid T=7 icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B, C [auth A], D, E	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
A [auth C], B, C [auth A], D, E	IPR000662	Capsid protein VP1,Polyomavirus	Family
A [auth C], B, C [auth A], D, E	IPR036931	Polyomavirus capsid protein VP1 superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.