1JMA | pdb_00001jma

CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS GLYCOPROTEIN D BOUND TO THE CELLULAR RECEPTOR HVEA/HVEM

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth A]	d1jmaa_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	HSV glycoprotein D	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth B]	d1jmab2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Cellular receptor HveA, C-terminal domain	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)
A [auth B]	d1jmab1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Cellular receptor HveA, N-terminal domain	Herpes simplex virus type 1 (Human alphaherpesvirus 1 ) [TaxId: 10298 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2 Family	V set domains-like	8054516	4007530	SCOP2 (2022-06-29)
B [auth A]	SCOP2 Superfamily	Immunoglobulin (Ig) domain-like	8054517	3000071	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Family	TNF receptor-like	8022126	4003512	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Family	TNF receptor-like	8022128	4003512	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	TNF receptor-like	8034506	3000971	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	TNF receptor-like	8034508	3000971	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)
B [auth A]	Herpes_glycop_D	e1jmaA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Herpes_glycop_D	ECOD (1.6)
A [auth B]	TNFR_c6	e1jmaB1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6	ECOD (1.6)
A [auth B]	TNFRSF14	e1jmaB2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFRSF14	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	2.70.230.10	Mainly Beta	Distorted Sandwich	Glycoprotein D	Chain: A	CATH (4.2.0)
A [auth B]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	GLYCOPROTEIN D	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 entry receptor-mediated virion attachment 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 entry into host cell symbiont entry into host	virion component viral membrane viral envelope cellular anatomical structure membrane virion membrane host cellular component host intracellular part host cell cytoplasm host cell part host cell Golgi apparatus host intracellular region other organism part host cell cytoplasm part
A [auth B]	HERPESVIRUS ENTRY MEDIATOR	protein binding binding cytokine binding virus receptor activity exogenous protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity tumor necrosis factor receptor activity death receptor activity molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity protein binding binding cytokine binding virus receptor activity exogenous protein binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity tumor necrosis factor receptor activity death receptor activity molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response immune system process adaptive immune response positive regulation of locomotion cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cellular process signal transduction cell communication immune response immune system process adaptive immune response positive regulation of locomotion regulation of cell motility positive regulation of biological process regulation of lymphocyte migration positive regulation of cell migration positive regulation of cell motility regulation of cell migration positive regulation of mononuclear cell migration cell migration regulation of immune system process cell motility regulation of mononuclear cell migration positive regulation of immune system process locomotion positive regulation of cellular process positive regulation of lymphocyte migration regulation of leukocyte migration positive regulation of T cell migration lymphocyte migration positive regulation of leukocyte migration leukocyte migration regulation of locomotion regulation of T cell migration mononuclear cell migration T cell migration biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium response to bacterium response to stress response to external biotic stimulus adaptive immune memory response regulation of adaptive immune response negative regulation of response to stimulus negative regulation of immune response negative regulation of biological process negative regulation of adaptive immune response negative regulation of adaptive immune memory response regulation of adaptive immune memory response regulation of response to stimulus negative regulation of immune system process regulation of immune response immunological memory process multicellular organismal process regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation defense response to symbiont defense response to other organism innate immune response negative regulation of lymphocyte proliferation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation negative regulation of lymphocyte activation leukocyte proliferation negative regulation of mononuclear cell proliferation negative regulation of cellular process T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation negative regulation of cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of immune effector process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of immune effector process positive regulation of macromolecule metabolic process cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of cytokine production involved in immune response regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process immune effector process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process regulation of alpha-beta T cell activation alpha-beta T cell proliferation alpha-beta T cell activation regulation of alpha-beta T cell proliferation negative regulation of alpha-beta T cell proliferation negative regulation of alpha-beta T cell activation defense response to Gram-positive bacterium	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth A]	IPR002896	Herpesvirus glycoprotein D/GG/GX domain	Domain
A [auth B]	IPR022332	Tumour necrosis factor receptor 14	Family
A [auth B]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
A [auth B]	IPR034031	Tumor necrosis factor receptor 14/UL144, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: Q92956	rheumatoid arthritis celiac disease allergic rhinitis Brain Injuries, Focal Hashimoto thyroiditis large cell medulloblastoma primary biliary cholangitis ulcerative colitis azoospermia brain injury diffuse large B-cell lymphoma hypothyroidism osteosarcoma follicular lymphoma pancreatic ductal adenocarcinoma rheumatoid arthritis celiac disease allergic rhinitis Brain Injuries, Focal Hashimoto thyroiditis large cell medulloblastoma primary biliary cholangitis ulcerative colitis azoospermia brain injury diffuse large B-cell lymphoma hypothyroidism osteosarcoma follicular lymphoma pancreatic ductal adenocarcinoma sclerosing cholangitis

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.