4GKO

Crystal structure of the calcium2+-bound human IgE-Fc(epsilon)3-4 bound to its B cell receptor derCD23

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)
G	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	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	PF07654	e4gkoA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B	PF07654	e4gkoB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C	PF07654	e4gkoC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D	PF07654	e4gkoD4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F	PF07654	e4gkoF6	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E	PF07654	e4gkoE4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G	PF00059	e4gkoG1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
H	PF00059	e4gkoH1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
I	PF00059	e4gkoI1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
J	PF00059	e4gkoJ1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
K	PF00059	e4gkoK1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)
L	PF00059	e4gkoL1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: PF00059	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
H	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
I	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
J	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
K	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
L	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	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
A, B, C, D, E A, B, C, D, E, F	Ig epsilon chain C region	CH3-CH4	Homo sapiens (human)	IGHE01, IGHE02, IGHE*04	C-DOMAIN CH3, C-DOMAIN CH4	IG	(CH3-CH4_CH3-CH4)	IMGT (202413-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
G, H, I, J, K G, H, I, J, K, L	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	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	Ig epsilon chain C region	protein binding binding signaling receptor binding immunoglobulin receptor binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell antigen processing and presentation response to stimulus immune response adaptive immune response immune effector process antigen processing and presentation immune system process B cell mediated immunity leukocyte mediated immunity myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell antigen processing and presentation response to stimulus immune response adaptive immune response immune effector process antigen processing and presentation immune system process B cell mediated immunity leukocyte mediated immunity myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus immunoglobulin mediated immune response type II hypersensitivity type IIa hypersensitivity cellular process inflammatory response cell killing 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 antigen receptor-mediated signaling pathway activation of immune response humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin complement activation, classical pathway primary adaptive immune response biological process involved in interspecies interaction between organisms response to other organism antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation mononuclear cell proliferation lymphocyte proliferation regulated exocytosis cellular localization transport eosinophil activation cell activation involved in immune response leukocyte degranulation vesicle-mediated transport myeloid leukocyte activation localization secretion by cell establishment of localization in cell leukocyte activation involved in immune response eosinophil degranulation eosinophil activation involved in immune response secretion export from cell establishment of localization myeloid cell activation involved in immune response exocytosis eosinophil mediated immunity granulocyte activation establishment of organelle localization organelle localization mast cell activation mast cell mediated immunity vacuolar localization mast cell degranulation mast cell activation involved in immune response lysosome localization developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis macrophage differentiation cell development myeloid cell differentiation cell differentiation anatomical structure development leukocyte differentiation type 2 immune response import into cell Fc receptor-mediated immune complex endocytosis receptor-mediated endocytosis endocytosis protein-containing complex localization adaptive immune memory response immunological memory process type I hypersensitivity macrophage activation	cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex IgE immunoglobulin complex immunoglobulin complex extracellular region extracellular space immunoglobulin complex, circulating plasma membrane protein complex membrane protein complex IgE B cell receptor complex receptor complex cell periphery plasma membrane membrane cellular anatomical entity protein-containing complex IgE immunoglobulin complex immunoglobulin complex extracellular region extracellular space immunoglobulin complex, circulating plasma membrane protein complex membrane protein complex IgE B cell receptor complex receptor complex B cell receptor complex plasma membrane signaling receptor complex
G, H, I, J, K G, H, I, J, K, L	Low affinity immunoglobulin epsilon Fc receptor	binding carbohydrate binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding IgE binding immunoglobulin binding molecular transducer activity immunoglobulin receptor activity transmembrane signaling receptor activity signaling receptor activity low-affinity IgE receptor activity binding carbohydrate binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding IgE binding immunoglobulin binding molecular transducer activity immunoglobulin receptor activity transmembrane signaling receptor activity signaling receptor activity low-affinity IgE receptor activity immune receptor activity IgE receptor activity cation binding ion binding metal ion binding small molecule binding	regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process regulation of nitric-oxide synthase biosynthetic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process nitric-oxide synthase biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process regulation of nitric-oxide synthase biosynthetic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process nitric-oxide synthase biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process regulation of cellular biosynthetic process biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process positive regulation of nitric-oxide synthase biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity B cell antigen processing and presentation response to stimulus immune response adaptive immune response immune effector process antigen processing and presentation immune system process B cell mediated immunity leukocyte mediated immunity regulation of catalytic activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity positive regulation of nitric-oxide synthase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of nitric-oxide synthase activity localization import into cell Fc receptor-mediated immune complex endocytosis transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport protein-containing complex localization biological process involved in interspecies interaction between organisms positive regulation of programmed cell death positive regulation of killing of cells of another organism regulation of killing of cells of another organism disruption of cell in another organism regulation of programmed cell death cell death regulation of cell killing positive regulation of cell killing disruption of anatomical structure in another organism modulation of process of another organism programmed cell death killing of cells of another organism cell killing regulation of humoral immune response regulation of immune effector process humoral immune response positive regulation of leukocyte mediated immunity regulation of humoral immune response mediated by circulating immunoglobulin positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of B cell mediated immunity positive regulation of response to stimulus humoral immune response mediated by circulating immunoglobulin positive regulation of humoral immune response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune response regulation of immunoglobulin mediated immune response regulation of immune system process positive regulation of immune effector process positive regulation of adaptive immune response positive regulation of immune system process positive regulation of immunoglobulin mediated immune response positive regulation of humoral immune response mediated by circulating immunoglobulin regulation of adaptive immune response immunoglobulin mediated immune response regulation of B cell mediated immunity regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity regulation of response to stimulus regulation of immune response macrophage activation multicellular organismal process cell activation myeloid leukocyte activation leukocyte activation	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003597	Immunoglobulin C1-set	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR007110	Immunoglobulin-like domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR016187	C-type lectin fold	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR033989	CD209-like, C-type lectin-like domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR001304	C-type lectin-like	Domain
G, H, I, J, K G, H, I, J, K, L	IPR018378	C-type lectin, conserved site	Conserved Site
G, H, I, J, K G, H, I, J, K, L	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P01854	asthma seasonal allergic rhinitis Chronic idiopathic urticaria psoriasis
G, H, I, J, K G, H, I, J, K, L	Pharos: P06734	encephalitis HIV infectious disease B-cell chronic lymphocytic leukemia large cell medulloblastoma psoriasis Hypersensitivity, Immediate medulloblastoma osteosarcoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.