8YGR | pdb_00008ygr

Cryo-EM structure of partial VP4 from simian rotavirus SA11

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	LRR_1, LRR_5, LRR_6, LRR_8	e8ygrC01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.1)
B	LRR_1, LRR_5, LRR_6, LRR_8	e8ygrB01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.1)
A	LRR_1, LRR_5, LRR_6, LRR_8	e8ygrA01	A: a/b three-layered sandwiches	X: ATP-grasp_6	H: ATP-grasp_6	T: ATP-grasp_6	F: LRR_1, LRR_5, LRR_6, LRR_8	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00426	Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain (VP4_haemagglut)	Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain	This entry represents the N-terminal concanavalin-like domain from the VP4 protein of rotavirus.	Domain
B	PF17477	Rotavirus VP4 membrane interaction domain (Rota_VP4_MID)	Rotavirus VP4 membrane interaction domain	This entry represents the VP4 membrane interaction domain.	Domain
A	PF17478	Rotavirus VP4 helical domain (VP4_helical)	Rotavirus VP4 helical domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	Outer capsid protein VP4	-	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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell 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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism	host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane viral capsid icosahedral viral capsid virion component viral outer capsid host cell endoplasmic reticulum host cell rough endoplasmic reticulum
B	Outer capsid protein VP4	-	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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell 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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism	host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane viral capsid icosahedral viral capsid virion component viral outer capsid host cell endoplasmic reticulum host cell rough endoplasmic reticulum
A	Outer capsid protein VP4	-	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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell 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-mediated disruption of host anatomical structure symbiont entry into host cell via permeabilization of host membrane symbiont-mediated disruption of host cellular anatomical structure symbiont-mediated perturbation of host membrane permeabilization of host organelle membrane involved in viral entry into host cell symbiont entry into host cell symbiont entry into host disruption of anatomical structure in another organism	host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cell membrane viral capsid icosahedral viral capsid virion component viral outer capsid host cell endoplasmic reticulum host cell rough endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
C	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
C	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
C	IPR035329	Rotavirus VP4 helical domain	Domain
C	IPR042546	Outer capsid protein VP4	Family
C	IPR038017	Rotavirus VP4, membrane interaction domain superfamily	Homologous Superfamily
B	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
B	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B	IPR035329	Rotavirus VP4 helical domain	Domain
B	IPR042546	Outer capsid protein VP4	Family
B	IPR038017	Rotavirus VP4, membrane interaction domain superfamily	Homologous Superfamily
A	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
A	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR035329	Rotavirus VP4 helical domain	Domain
A	IPR042546	Outer capsid protein VP4	Family
A	IPR038017	Rotavirus VP4, membrane interaction domain 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.