6Y5X | pdb_00006y5x

Structure of apo New Jersey Polyomavirus VP1

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)
A	d6y5xa_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
B	d6y5xb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
C	d6y5xc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
D	d6y5xd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
E	d6y5xe_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
F	d6y5xf_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
G	d6y5xg_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
H	d6y5xh_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
I	d6y5xi_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
J	d6y5xj_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
G	SCOP2 Family	papovaviridae-like vp	8096007	4003485	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group I dsDNA viruses	8096008	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)
A	Bac_rhodopsin	e6y5xA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
B	Bac_rhodopsin	e6y5xB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
C	Bac_rhodopsin	e6y5xC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
D	Bac_rhodopsin	e6y5xD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
E	Bac_rhodopsin	e6y5xE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
F	Bac_rhodopsin	e6y5xF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
G	Bac_rhodopsin	e6y5xG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
H	Bac_rhodopsin	e6y5xH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
I	Bac_rhodopsin	e6y5xI1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)
J	Bac_rhodopsin	e6y5xJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Bac_rhodopsin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
B	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
C	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
D	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
E	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
F	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
G	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
H	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
I	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
J	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	VP1	structural molecule activity cation binding ion binding binding metal ion binding small molecule binding	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host endocytosis involved in viral entry into host cell	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, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000662	Capsid protein VP1,Polyomavirus	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	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.