4V7Q | pdb_00004v7q

Atomic model of an infectious rotavirus particle

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth AB]	SCOP2B Superfamily	Reovirus inner layer core protein p3	8094216	3001935	SCOP2B (2022-06-29)
A [auth AA]	SCOP2 Family	Rotavirus core (VP2)	8046844	4005324	SCOP2 (2022-06-29)
A [auth AA]	SCOP2 Superfamily	Reovirus inner layer core protein p3	8094216	3001935	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
EA [auth BZ]	LHC	e4v7qBZ1	A: alpha arrays	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: LHC	ECOD (v295)
DA [auth BY]	LHC	e4v7qBY1	A: alpha arrays	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: LHC	ECOD (v295)
CA [auth BX]	Rota_VP4_MID	e4v7qBX1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
CA [auth BX]	LHC	e4v7qBX2	A: alpha arrays	X: Type III secretion system domain-like	H: Antibiotic binding domain of TipA-like multidrug resistance regulators	T: Antibiotic binding domain of TipA-like multidrug resistance regulators	F: LHC	ECOD (v295)
Z [auth BO]	Rota_VP4_MID	e4v7qBO1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
Y [auth BN]	Rota_VP4_MID	e4v7qBN1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
X [auth BM]	Rota_VP4_MID	e4v7qBM1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
W [auth BL]	Rota_VP4_MID	e4v7qBL1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
V [auth BK]	Rota_VP4_MID	e4v7qBK1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
U [auth BJ]	Rota_VP4_MID	e4v7qBJ1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
T [auth BI]	Rota_VP4_MID	e4v7qBI1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
S [auth BH]	Rota_VP4_MID	e4v7qBH1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
R [auth BG]	Rota_VP4_MID	e4v7qBG1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
Q [auth BF]	Rota_VP4_MID	e4v7qBF1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
P [auth BA]	Rota_VP4_MID	e4v7qBA1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
BA [auth BQ]	Rota_VP4_MID	e4v7qBQ1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
AA [auth BP]	Rota_VP4_MID	e4v7qBP1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
O [auth AO]	Rota_VP4_MID	e4v7qAO1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
N [auth AN]	Rota_VP4_MID	e4v7qAN1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
M [auth AM]	Rota_VP4_MID	e4v7qAM1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
L [auth AL]	Rota_VP4_MID	e4v7qAL1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
K [auth AK]	Rota_VP4_MID	e4v7qAK1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
J [auth AJ]	Rota_VP4_MID	e4v7qAJ1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
I [auth AI]	Rota_VP4_MID	e4v7qAI1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
H [auth AH]	Rota_VP4_MID	e4v7qAH1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
G [auth AG]	Rota_VP4_MID	e4v7qAG1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
F [auth AF]	Rota_VP4_MID	e4v7qAF1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
E [auth AE]	Rota_VP4_MID	e4v7qAE1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
D [auth AD]	Rota_VP4_MID	e4v7qAD1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
C [auth AC]	Rota_VP4_MID	e4v7qAC1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
B [auth AB]	Rota_VP4_MID	e4v7qAB1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)
A [auth AA]	Rota_VP4_MID	e4v7qAA1	A: alpha arrays	X: VP4 membrane interaction domain	H: VP4 membrane interaction domain	T: VP4 membrane interaction domain	F: Rota_VP4_MID	ECOD (v295)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
CA [auth BX], DA [auth BY], EA [auth BZ]	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
AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], S [auth BH], T [auth BI], U [auth BJ], V [auth BK], W [auth BL], X [auth BM], Y [auth BN], Z [auth BO]	Outer layer protein VP7	cation binding ion binding binding metal ion binding small molecule binding	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell 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	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endoplasmic reticulum lumen host intracellular region viral capsid icosahedral viral capsid host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endoplasmic reticulum lumen host intracellular region viral capsid icosahedral viral capsid virion component viral outer capsid T=13 icosahedral viral capsid
C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO]	Intermediate capsid protein VP6	structural molecule activity cation binding ion binding binding metal ion binding small molecule binding host cell surface binding host cell surface receptor binding	membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane viral process cellular process cellular component organization or biogenesis membrane fusion involved in viral entry into host cell	virion component viral membrane viral envelope viral capsid icosahedral viral capsid T=13 icosahedral viral capsid viral intermediate capsid
A [auth AA], B [auth AB]	Core scaffold protein	RNA binding binding nucleic acid binding	-	viral capsid icosahedral viral capsid virion component viral inner capsid viral nucleocapsid T=2 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR035329	Rotavirus VP4 helical domain	Domain
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR042546	Outer capsid protein VP4	Family
CA [auth BX], DA [auth BY], EA [auth BZ]	IPR038017	Rotavirus VP4, membrane interaction domain superfamily	Homologous Superfamily
AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], S [auth BH], T [auth BI], U [auth BJ], V [auth BK], W [auth BL], X [auth BM], Y [auth BN], Z [auth BO]	IPR042207	Glycoprotein VP7, domain 1	Homologous Superfamily
AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], S [auth BH], T [auth BI], U [auth BJ], V [auth BK], W [auth BL], X [auth BM], Y [auth BN], Z [auth BO]	IPR001963	Glycoprotein VP7	Family
AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], AA [auth BP], BA [auth BQ], P [auth BA], Q [auth BF], R [auth BG], S [auth BH], T [auth BI], U [auth BJ], V [auth BK], W [auth BL], X [auth BM], Y [auth BN], Z [auth BO]	IPR042210	Glycoprotein VP7, domain 2	Homologous Superfamily
C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO]	IPR001385	Rotavirus A/C, major capsid protein VP6	Family
C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO]	IPR008935	Virus capsid protein, alpha-helical	Homologous Superfamily
C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], C [auth AC], D [auth AD], E [auth AE], F [auth AF], G [auth AG], H [auth AH], I [auth AI], J [auth AJ], K [auth AK], L [auth AL], M [auth AM], N [auth AN], O [auth AO]	IPR008980	Viral capsid/haemagglutinin protein	Homologous Superfamily
A [auth AA], B [auth AB]	IPR007779	Rotavirus VP2	Family

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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.