5CQ0 | pdb_00005cq0

Crystal structure of murine polyomavirus RA strain VP1 in complex with the GD1a glycan

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	d5cq0e_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	Polyomavirus coat proteins	MPyV (Mouse polyomavirus (strain p16 small-plaque) ) [TaxId: 47935 ],	SCOPe (2.08)
D	d5cq0d_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	Polyomavirus coat proteins	MPyV (Mouse polyomavirus (strain p16 small-plaque) ) [TaxId: 47935 ],	SCOPe (2.08)
C	d5cq0c_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	Polyomavirus coat proteins	MPyV (Mouse polyomavirus (strain p16 small-plaque) ) [TaxId: 47935 ],	SCOPe (2.08)
B	d5cq0b_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	Polyomavirus coat proteins	MPyV (Mouse polyomavirus (strain p16 small-plaque) ) [TaxId: 47935 ],	SCOPe (2.08)
A	d5cq0a_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	Polyomavirus coat proteins	MPyV (Mouse polyomavirus (strain p16 small-plaque) ) [TaxId: 47935 ],	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	8040828	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8040828	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8040828	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8040828	3000939	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group I dsDNA viruses	8040828	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	HIT	e5cq0E1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: HIT	ECOD (v294.1)
D	HIT	e5cq0D1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: HIT	ECOD (v294.1)
C	HIT	e5cq0C1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: HIT	ECOD (v294.1)
B	HIT	e5cq0B1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: HIT	ECOD (v294.1)
A	HIT	e5cq0A1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: HIT	ECOD (v294.1)

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	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	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, B, C, D, E	Capsid protein VP1	structural molecule activity	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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization caveolin-mediated endocytosis vesicle-mediated transport 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 import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization caveolin-mediated endocytosis vesicle-mediated transport localization symbiont entry into host cell caveolin-mediated endocytosis of virus by host cell symbiont entry into host cellular process endocytosis involved in viral entry into host cell receptor-mediated endocytosis endocytosis	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	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
A, B, C, D, E	IPR000662	Capsid protein VP1,Polyomavirus	Family
A, B, C, 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.