7XQ8 | pdb_00007xq8

Structure of human B-cell antigen receptor of the IgM isotype

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth R]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	SCOP2B (2022-06-29)
B [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	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)
D [auth R]	C1-set_4	e7xq8R1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth R]	V-set	e7xq8R2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth L]	C1-set_4	e7xq8L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B [auth L]	V-set	e7xq8L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L], D [auth R]	Light Chain	IGKV3	Kappa	-	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth B]	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
E [auth A]	PF13927	Immunoglobulin domain (Ig_3)	Immunoglobulin domain	This family contains immunoglobulin-like domains.	Domain
B [auth L], D [auth R]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
A [auth C], C [auth v]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth B]	B-cell antigen receptor complex-associated protein beta chain	identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	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 immune system process anatomical structure development 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 immune system process anatomical structure development cellular process leukocyte differentiation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response biological process involved in interspecies interaction between organisms response to other organism response to bacterium response to external stimulus response to external biotic stimulus response to biotic stimulus	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex IgM immunoglobulin complex plasma membrane protein complex IgM B cell receptor complex membrane protein complex immunoglobulin complex receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex IgM immunoglobulin complex plasma membrane protein complex IgM B cell receptor complex membrane protein complex immunoglobulin complex receptor complex B cell receptor complex plasma membrane signaling receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle
E [auth A]	B-cell antigen receptor complex-associated protein alpha chain	identical protein binding protein binding binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process developmental process cellular developmental process multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation immune system process lymphocyte proliferation cellular process developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response adaptive immune response	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex IgM immunoglobulin complex plasma membrane protein complex IgM B cell receptor complex membrane protein complex immunoglobulin complex receptor complex cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane protein-containing complex IgM immunoglobulin complex plasma membrane protein complex IgM B cell receptor complex membrane protein complex immunoglobulin complex receptor complex B cell receptor complex plasma membrane signaling receptor complex membrane microdomain membrane raft membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle late endosome cytoplasm multivesicular body vesicle
B [auth L], D [auth R]	Light chain of Fab fragments of the VRC01 antibody,Immunoglobulin kappa constant	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
A [auth C], C [auth v]	Chimera of Heavy chain of VRC01 antibody Fab and Isoform 2 of Immunoglobulin heavy constant mu	binding antigen binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response 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 humoral immune response antibacterial humoral response defense response to symbiont antimicrobial humoral response defense response to other organism innate immune response multicellular organismal process cellular developmental process immature B cell differentiation cell development mononuclear cell differentiation pre-B cell allelic exclusion pre-B cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development developmental process regulation of biosynthetic process hemopoiesis B cell activation cell activation regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process leukocyte differentiation	hexameric IgM immunoglobulin complex protein-containing complex cellular anatomical structure IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex hexameric IgM immunoglobulin complex protein-containing complex cellular anatomical structure IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex membrane protein complex receptor complex B cell receptor complex cell periphery plasma membrane signaling receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle pentameric IgM immunoglobulin complex cell surface

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth B]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F [auth B]	IPR013106	Immunoglobulin V-set domain	Domain
F [auth B]	IPR003599	Immunoglobulin domain subtype	Domain
F [auth B]	IPR007110	Immunoglobulin-like domain	Domain
F [auth B]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
E [auth A]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth A]	IPR003598	Immunoglobulin subtype 2	Domain
E [auth A]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth A]	IPR003599	Immunoglobulin domain subtype	Domain
E [auth A]	IPR007110	Immunoglobulin-like domain	Domain
E [auth A]	IPR003110	Phosphorylated immunoreceptor signalling ITAM	Repeat
B [auth L], D [auth R]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L], D [auth R]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth L], D [auth R]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L], D [auth R]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L], D [auth R]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L], D [auth R]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth C], C [auth v]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth C], C [auth v]	IPR050380	Immune Recognition and Response Modulators	Family
A [auth C], C [auth v]	IPR003597	Immunoglobulin C1-set	Domain
A [auth C], C [auth v]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth C], C [auth v]	IPR007110	Immunoglobulin-like domain	Domain
A [auth C], C [auth v]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
F [auth B]	Pharos: P40259	agammaglobulinemia 6, autosomal recessive diffuse large B-cell lymphoma agammaglobulinemia liver disease autosomal recessive agammaglobulinemia 1 Hypogammaglobulinemia non-Hodgkin lymphoma interstitial cystitis lymphoma osteosarcoma autosomal agammaglobulinemia nasopharyngeal carcinoma pituitary cancer
E [auth A]	Pharos: P11912	agammaglobulinemia diffuse large B-cell lymphoma agammaglobulinemia 3, autosomal recessive autosomal recessive agammaglobulinemia 1 Hypogammaglobulinemia lymphoma osteosarcoma sinusitis cutaneous lupus erythematosus gastric cancer interstitial cystitis non-Hodgkin lymphoma pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis autosomal agammaglobulinemia agammaglobulinemia diffuse large B-cell lymphoma agammaglobulinemia 3, autosomal recessive autosomal recessive agammaglobulinemia 1 Hypogammaglobulinemia lymphoma osteosarcoma sinusitis cutaneous lupus erythematosus gastric cancer interstitial cystitis non-Hodgkin lymphoma pancreatic intraductal papillary-mucinous carcinoma ulcerative colitis autosomal agammaglobulinemia cystic fibrosis gastric carcinoma lung adenocarcinoma non-small cell lung carcinoma periodontitis
B [auth L], D [auth R]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency
A [auth C], C [auth v]	Pharos: P01871	autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm sinusitis ulcerative colitis autosomal agammaglobulinemia Bruton-type agammaglobulinemia Hypogammaglobulinemia lung cancer malignant pancreatic neoplasm osteosarcoma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth C], B [auth L], C [auth v], D [auth R], E [auth A] A [auth C], B [auth L], C [auth v], D [auth R], E [auth A], F [auth B]	OPM	Transmembrane	Bitopic proteins	T-cell and B-cell receptor complexes	B-cell antigen receptor complex

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth C], B [auth L], C [auth v], D [auth R], E [auth A] A [auth C], B [auth L], C [auth v], D [auth R], E [auth A], F [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	B Cell Receptor Complexes	B-Cell receptor in complex with IgM