8SM0 | pdb_00008sm0

Crystal structure of human complement receptor 2 (CD21) in complex with Epstein-Barr virus major glycoprotein gp350

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
A [auth C]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8032835	3000902	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Sushi/CCP/SCR domain	8032838	3000902	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C]	PF00084	Sushi repeat (SCR repeat) (Sushi)	Sushi repeat (SCR repeat)		Domain
B [auth G]	PF20676	Herpesvirus envelope glycoprotein gp350, N-terminal B domain (Herpes_gp350_B)	Herpesvirus envelope glycoprotein gp350, N-terminal B domain	This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible ...	This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo [1]. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C-terminal that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A, B and C) which organise into an "L-shape" structure. This is domain B [2].	Domain
B [auth G]	PF20677	Herpesvirus envelope glycoprotein gp350 N-terminal C domain (Herpes_gp350_C)	Herpesvirus envelope glycoprotein gp350 N-terminal C domain	This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible ...	This entry consists of the envelope glycoprotein gp350 from Epstein-Barr virus (also known as BLLF1 viral late glycoprotein). It is the most abundantly expressed glycoprotein in the viral envelope of Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo [1]. It is a 907 residues long gp350 polypeptide containing an 18-residue peptide at the C-terminal that is located inside the viral membrane, a membrane-spanning domain and a large N-terminal segment (860 residues) predicted to extend outside the viral membrane. The extreme N-terminal region (1-470) is sufficient to bind receptor CR2 (also known as CD21) and fold into three distinct domains (denoted as A, B and C) which organise into an "L-shape" structure. This is domain C [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	Complement receptor type 2	protein binding binding virus receptor activity exogenous protein binding molecular transducer activity complement receptor activity transmembrane signaling receptor activity signaling receptor activity immune receptor activity complement binding signaling receptor binding immunoglobulin receptor binding DNA binding nucleic acid binding protein binding binding virus receptor activity exogenous protein binding molecular transducer activity complement receptor activity transmembrane signaling receptor activity signaling receptor activity immune receptor activity complement binding signaling receptor binding immunoglobulin receptor binding DNA binding nucleic acid binding identical protein binding protein homodimerization activity protein dimerization activity	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity response to stimulus immune response immune system process leukocyte mediated immunity adaptive immune response immune effector process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity response to stimulus immune response immune system process leukocyte mediated immunity adaptive immune response immune effector process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development cellular process leukocyte differentiation humoral immune response positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process biological regulation immunoglobulin mediated immune response regulation of response to stimulus B cell mediated immunity regulation of immune response activation of immune response biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction regulation of humoral immune response regulation of immune effector process regulation of humoral immune response mediated by circulating immunoglobulin negative regulation of biological process negative regulation of lymphocyte mediated immunity negative regulation of complement activation, classical pathway negative regulation of B cell mediated immunity regulation of adaptive immune response negative regulation of immune response negative regulation of immune effector process negative regulation of humoral immune response negative regulation of adaptive immune response regulation of B cell mediated immunity negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of leukocyte mediated immunity negative regulation of immunoglobulin mediated immune response regulation of complement activation, classical pathway regulation of complement activation negative regulation of complement activation regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of immunoglobulin mediated immune response negative regulation of response to stimulus negative regulation of humoral immune response mediated by circulating immunoglobulin regulation of lymphocyte mediated immunity negative regulation of immune system process negative regulation of leukocyte mediated immunity cell population proliferation B cell proliferation leukocyte proliferation mononuclear cell proliferation lymphocyte proliferation complement activation, alternative pathway response to biotic stimulus response to stress innate immune response response to external biotic stimulus response to other organism defense response defense response to symbiont response to external stimulus defense response to other organism cellular response to stimulus regulation of cellular process signaling response to cytokine cytokine-mediated signaling pathway cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus signal transduction cell surface receptor signaling pathway response to peptide response to chemical type I interferon-mediated signaling pathway response to type I interferon	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane protein-containing complex cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane protein-containing complex receptor complex
B [auth G]	Envelope glycoprotein gp350	molecular transducer activity protein binding binding molecular function activator activity signaling receptor binding signaling receptor activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	host cellular component cellular anatomical structure host cell part host cell membrane membrane virion component virion membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C]	IPR051277	SEZ6/CSMD/C4BPB Neuronal & Immune Regulators	Family
A [auth C]	IPR000436	Sushi/SCR/CCP domain	Domain
A [auth C]	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily
B [auth G]	IPR048700	Envelope glycoprotein GP350, N-terminal, A domain, herpervirus superfamily	Homologous Superfamily
B [auth G]	IPR007796	Envelope glycoprotein GP350, N-terminal, A domain, herpervirus	Domain
B [auth G]	IPR048689	Envelope glycoprotein GP350, N-terminal, B domain, herpervirus	Domain
B [auth G]	IPR048692	Envelope glycoprotein GP350, N-terminal, C domain, herpesvirus	Domain
B [auth G]	IPR048698	Envelope glycoprotein GP350, N-terminal, C domain, herpesvirus superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C]	Pharos: P20023	common variable immunodeficiency systemic lupus erythematosus agammaglobulinemia immunodeficiency, common variable, 7 Acquired Hypogammaglobulinemia B cell deficiency immunodeficiency, common variable, 2 interstitial cystitis lupus erythematosus lymphoplasmacytic lymphoma osteosarcoma systemic lupus erythematosus, susceptibility to, 9 nasopharyngeal carcinoma Sjogren syndrome ulcerative colitis common variable immunodeficiency systemic lupus erythematosus agammaglobulinemia immunodeficiency, common variable, 7 Acquired Hypogammaglobulinemia B cell deficiency immunodeficiency, common variable, 2 interstitial cystitis lupus erythematosus lymphoplasmacytic lymphoma osteosarcoma systemic lupus erythematosus, susceptibility to, 9 nasopharyngeal carcinoma Sjogren syndrome ulcerative colitis Alzheimer disease hematologic disease lung adenocarcinoma lymphatic system disease non-small cell lung carcinoma

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.