5YMT | pdb_00005ymt

Functional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens

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)
N	d5ymtn_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
M	d5ymtm_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
L	d5ymtl_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
K	d5ymtk_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
J	d5ymtj_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
I	d5ymti_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
H	d5ymth_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
G	d5ymtg_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
F	d5ymtf_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
E	d5ymte_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
D	d5ymtd_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
C	d5ymtc_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
B	d5ymtb_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)
A	d5ymta_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Human rotavirus A ) [TaxId: 10941 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077020	3000120	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)
N	VP4_haemagglut	e5ymtN1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
M	VP4_haemagglut	e5ymtM1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
L	VP4_haemagglut	e5ymtL1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
K	VP4_haemagglut	e5ymtK1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
J	VP4_haemagglut	e5ymtJ1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
I	VP4_haemagglut	e5ymtI1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
H	VP4_haemagglut	e5ymtH1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
G	VP4_haemagglut	e5ymtG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
F	VP4_haemagglut	e5ymtF1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
E	VP4_haemagglut	e5ymtE1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
D	VP4_haemagglut	e5ymtD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
C	VP4_haemagglut	e5ymtC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
B	VP4_haemagglut	e5ymtB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
A	VP4_haemagglut	e5ymtA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
M	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
L	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
K	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
J	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
I	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
H	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
G	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
F	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)

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, K, L, M, N	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

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, K, L, M, N	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 membrane host intracellular membrane-bounded organelle host cell cytoplasm part host cell endoplasmic reticulum-Golgi intermediate compartment host cell cytoplasm host cell plasma membrane host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle membrane 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
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR035329	Rotavirus VP4 helical domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR042546	Outer capsid protein VP4	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	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.