4GKO | pdb_00004gko

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)
L	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)
J	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)
H	SCOP2B Superfamily	C-type lectin-like	8032471	3001261	SCOP2B (2022-06-29)
G	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)
F		e4gkoF5	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
E		e4gkoE3	A: Subtilisin-like	X: Subtilisin-like	H: Subtilisin-like	T: V-set	F:	ECOD (20:10:01)
D		e4gkoD3	A: Fusion glycoprotein F2	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Cadherin	F:	ECOD (20:10:01)
C		e4gkoC1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
B		e4gkoB1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
A		e4gkoA1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
L		e4gkoL1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
K		e4gkoK1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
J		e4gkoJ1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
I		e4gkoI1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
H		e4gkoH1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)
G		e4gkoG1	A: PBZ domain	X: PBZ domain	H: PBZ domain	T: Kringle	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
D	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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	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)
J	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)
H	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
G	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 (202609-0)

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 B cell activation cell activation lymphocyte activation leukocyte activation cell population proliferation B cell proliferation leukocyte proliferation 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 cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development mononuclear cell differentiation leukocyte differentiation myeloid leukocyte differentiation macrophage differentiation myeloid cell differentiation type 2 immune response import into cell Fc receptor-mediated immune complex endocytosis receptor-mediated endocytosis endocytosis adaptive immune memory response immunological memory process type I hypersensitivity macrophage activation	cell periphery cellular anatomical structure plasma membrane membrane 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 cellular anatomical structure plasma membrane membrane 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 enzyme binding protease binding IgE binding immunoglobulin binding molecular transducer activity immunoglobulin receptor activity transmembrane signaling receptor activity binding carbohydrate binding cell adhesion molecule binding protein-containing complex binding protein binding integrin binding signaling receptor binding enzyme binding protease 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 pattern recognition receptor activity cation binding ion binding metal ion binding small molecule 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 regulation of biosynthetic process regulation of biological process regulation of cellular 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 biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process localization import into cell Fc receptor-mediated immune complex endocytosis transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport 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 defense response to bacterium biological process involved in interspecies interaction between organisms response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus cellular response to stimulus immune response-regulating cell surface receptor signaling pathway signaling Fc-gamma receptor signaling pathway involved in phagocytosis cell communication immune response-activating signaling pathway Fc receptor signaling pathway immune response-regulating signaling pathway phagocytosis signal transduction Fc-gamma receptor signaling pathway cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway Fc receptor mediated stimulatory signaling pathway activation of immune response	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane 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	IPR050380	Immune Recognition and Response Modulators	Family
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
G, H, I, J, K G, H, I, J, K, L	IPR050111	C-type lectin and snaclec domain-containing protein	Family

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 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.