4POS

Structure of Human Polyomavirus 9 VP1 pentamer in complex with 3'-sialyllactosamine

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	d4posa_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
B	d4posb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
C	d4posc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
D	d4posd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
E	d4pose_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
F	d4posf_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
G	d4posg_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
H	d4posh_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
I	d4posi_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	SCOPe (2.08)
J	d4posj_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Human polyomavirus 9 ) [TaxId: 943908 ],	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	8081595	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group I dsDNA viruses	8081595	3000939	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group I dsDNA viruses	8081595	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	Polyoma_coat	e4posA1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
B	Polyoma_coat	e4posB1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
C	Polyoma_coat	e4posC1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
D	Polyoma_coat	e4posD1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
E	Polyoma_coat	e4posE1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
F	Polyoma_coat	e4posF1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
G	Polyoma_coat	e4posG1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
H	Polyoma_coat	e4posH1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
I	Polyoma_coat	e4posI1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
J	Polyoma_coat	e4posJ1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)

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 (4.3.0)
B	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
C	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)
E	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
F	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
G	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
H	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
I	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
J	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	PF00718	Polyomavirus coat protein (Polyoma_coat)	Polyomavirus coat protein	-	Domain

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	viral capsid icosahedral viral capsid T=7 icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell part host intracellular region cellular anatomical entity host cell nucleus 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 National Science Foundation (DBI-1832184), 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 R01GM133198.