4ODB

Crystal structure of the T1L reovirus attachment protein sigma1 in complex with Junctional Adhesion Molecule-A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054509	3000071	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054509	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054509	3000071	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)
A	Reo_sigma1_C,Reo_sigma1_N	e4odbA1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Reo_sigma1_C,Reo_sigma1_N	ECOD (1.6)
B	Reo_sigma1_C	e4odbB1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Reo_sigma1_C	ECOD (1.6)
C	Reo_sigma1_C	e4odbC1	A: beta sandwiches	X: Domain in virus attachment proteins (From Topology)	H: Domain in virus attachment proteins (From Topology)	T: Domain in virus attachment proteins	F: Reo_sigma1_C	ECOD (1.6)
D	I-set_12	e4odbD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_12	ECOD (1.6)
E	I-set_12	e4odbE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_12	ECOD (1.6)
F	I-set_12	e4odbF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.90.20	Mainly Beta	Sandwich	Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)	Virus attachment protein , globular domain	CATH (4.3.0)
B	2.60.90.20	Mainly Beta	Sandwich	Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)	Virus attachment protein , globular domain	CATH (4.3.0)
C	2.60.90.20	Mainly Beta	Sandwich	Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)	Virus attachment protein , globular domain	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
D, E, F	F11R (JAM, Junctional adhesion molecule A)	1V-LIKE	Homo sapiens (human)	F11R*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202436-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF01664	Reovirus viral attachment protein sigma 1 (Reo_sigma1)	Reovirus viral attachment protein sigma 1	-	Family
D, E, F	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Outer capsid protein sigma-1	-	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 cell adhesion cellular process symbiont entry into host cell symbiont entry into host	viral capsid virion component icosahedral viral capsid viral outer capsid
D, E, F	Junctional adhesion molecule A	protein binding binding virus receptor activity exogenous protein binding PDZ domain binding protein domain specific binding cell adhesion molecule binding protein-containing complex binding integrin binding signaling receptor binding identical protein binding protein homodimerization activity protein dimerization activity cadherin binding	T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cellular process cell motility T cell migration regulation of cytoskeleton organization regulation of cellular process regulation of cellular component organization T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cellular process cell motility T cell migration regulation of cytoskeleton organization regulation of cellular process regulation of cellular component organization regulation of actin filament-based process negative regulation of biological process regulation of actin filament bundle assembly cellular component biogenesis cellular component organization cellular component assembly actin filament bundle organization actin filament-based process negative regulation of cellular process cellular component organization or biogenesis stress fiber assembly negative regulation of supramolecular fiber organization regulation of biological process regulation of actin filament organization negative regulation of stress fiber assembly actin cytoskeleton organization actomyosin structure organization negative regulation of cellular component organization negative regulation of cytoskeleton organization biological regulation actin filament organization regulation of cellular component biogenesis negative regulation of actin filament bundle assembly regulation of organelle organization regulation of stress fiber assembly organelle organization negative regulation of organelle organization contractile actin filament bundle assembly regulation of actomyosin structure organization actin filament bundle assembly regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization cytoskeleton organization multicellular organismal process system process digestion intestinal absorption digestive system process developmental process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development establishment of endothelial intestinal barrier epithelial cell development cell differentiation establishment of endothelial barrier anatomical structure development cellular response to stimulus positive regulation of cell communication small GTPase-mediated signal transduction positive regulation of signal transduction response to stimulus signaling regulation of small GTPase mediated signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction Rho protein signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction regulation of response to stimulus regulation of cell communication positive regulation of small GTPase mediated signal transduction positive regulation of signaling protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane bicellular tight junction assembly regulation of bicellular tight junction assembly tight junction organization apical junction assembly regulation of cell junction assembly cell junction organization cell junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization regulation of body fluid levels homotypic cell-cell adhesion regulation of cell activation positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion response to stress coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of biological quality response to wounding wound healing regulation of homotypic cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion cell activation hemostasis platelet aggregation blood coagulation regulation of platelet activation regulation of platelet aggregation positive regulation of homotypic cell-cell adhesion positive regulation of platelet aggregation platelet activation regulation of biosynthetic process cellular biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of cytokine production cytokine production regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis regulation of anatomical structure morphogenesis response to mechanical stimulus response to external stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus leukocyte cell-cell adhesion maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis regulation of establishment of endothelial barrier positive regulation of endothelial cell development regulation of cell differentiation regulation of cell development regulation of epithelial cell differentiation positive regulation of developmental process multicellular organism development positive regulation of cell differentiation regulation of endothelial cell development regulation of multicellular organismal development regulation of endothelial cell differentiation positive regulation of cell development positive regulation of establishment of endothelial barrier defense response inflammatory response protein localization to bicellular tight junction protein localization to cell junction protein localization to cell-cell junction regulation of membrane permeability	cell junction cellular anatomical entity cell-cell junction anchoring junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery cell junction cellular anatomical entity cell-cell junction anchoring junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex apical junction complex bicellular tight junction tight junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR002592	Outer capsid protein sigma-1, C-terminal domain	Domain
A, B, C	IPR008982	Adenovirus pIV-like, attachment domain	Homologous Superfamily
D, E, F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D, E, F	IPR003598	Immunoglobulin subtype 2	Domain
D, E, F	IPR013106	Immunoglobulin V-set domain	Domain
D, E, F	IPR003599	Immunoglobulin domain subtype	Domain
D, E, F	IPR042456	Junctional adhesion molecule A	Family
D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D, E, F	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D, E, F	Pharos: Q9Y624	large cell medulloblastoma osteosarcoma lung cancer malignant mesothelioma

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 R01GM133198.