4EOW

Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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)
A [auth H]	d4eowh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4eowl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth L]	d4eowl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth H]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091519	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)
A [auth H]	PF07654	e4eowH2	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)
A [auth H]	PF07686	e4eowH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
B [auth L]	PF07654	e4eowL2	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 [auth L]	PF07686	e4eowL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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 [auth H]	MB007 human IgG1 Fab fragment	VH-CH1	Homo sapiens (human)	IGHV7-4-102, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ403, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)
B [auth L]	MB007 human IgG1 Fab fragment	L-LAMBDA	Homo sapiens (human)	IGLV1-4701, IGLJ201, IGLJ302, IGLJ301, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV7	-	-	SAbDab (2024-04-26)
B [auth L]	Light Chain	IGLV1	Lambda	-	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
B [auth L]	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
A [auth H]	MB007 human IgG1 Fab fragment heavy chain	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus immunoglobulin mediated immune response adaptive immune response immune effector process type II hypersensitivity immune system process type IIa hypersensitivity B cell mediated immunity 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 complement-dependent cytotoxicity 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	extracellular region extracellular space cellular anatomical entity blood microparticle protein-containing complex immunoglobulin complex, circulating immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle extracellular region extracellular space cellular anatomical entity blood microparticle protein-containing complex immunoglobulin complex, circulating 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
B [auth L]	MB007 IgG1 Fab fragment light chain	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	extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular region extracellular space cellular anatomical entity blood microparticle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth H]	IPR003597	Immunoglobulin C1-set	Domain
A [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth H]	IPR007110	Immunoglobulin-like domain	Domain
A [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
B [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth L]	IPR003597	Immunoglobulin C1-set	Domain
B [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth L]	IPR007110	Immunoglobulin-like domain	Domain
B [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth H]	Pharos: P01857	B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma B-cell chronic lymphocytic leukemia myositis polycystic ovary syndrome plasma cell myeloma plasma cell neoplasm Sclerocystic Ovaries acquired idiopathic inflammatory myopathy lung adenocarcinoma ovarian cancer peripheral neuropathy Sjogren syndrome amyloidosis breast cancer medulloblastoma nasopharyngeal carcinoma periodontitis interstitial cystitis myeloid neoplasm osteosarcoma peripheral nervous system disease

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.