7RK2 | pdb_00007rk2

Crystal structure of the human astrovirus serotype 8 capsid spike in complex with scFv 2D9, an astrovirus-neutralizing antibody, at 2.65-A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Norovirus P2 domain-like	8093103	3002678	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Norovirus P2 domain-like	8093103	3002678	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)
D	V-set_8	e7rk2D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D	V-set	e7rk2D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C	V-set_8	e7rk2C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	V-set	e7rk2C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B	Astro_capsid_p	e7rk2B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Astro_capsid_p	ECOD (1.6)
A	Astro_capsid_p	e7rk2A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Astro_capsid_p	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12226	Turkey astrovirus capsid protein (Astro_capsid_p)	Turkey astrovirus capsid protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	scFv 2D9	-	-	-
A, B	Capsid protein VP25	identical protein binding protein binding binding	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	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host extracellular space host cellular component cellular anatomical structure other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004337	Astrovirus capsid protein, inner core domain	Domain
A, B	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B	IPR022027	Turkey astrovirus capsid protein	Family

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.