6KN9

Crystal structure of human interleukin 18 receptor beta extracellular domain in complex with an antagonistic scFv

External Resource: Annotation

Domain Annotation: ECOD Classification
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	I-set_4	e6kn9A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_4	ECOD (1.6)
A	I-set_like	e6kn9A3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_like	ECOD (1.6)
A	I-set_16	e6kn9A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_16	ECOD (1.6)
B	I-set_4	e6kn9B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_4	ECOD (1.6)
B	I-set_like	e6kn9B3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_like	ECOD (1.6)
B	I-set_16	e6kn9B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_16	ECOD (1.6)
C	I-set_4	e6kn9C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_4	ECOD (1.6)
C	I-set_like	e6kn9C3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_like	ECOD (1.6)
C	I-set_16	e6kn9C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: I-set_16	ECOD (1.6)
D	V-set	e6kn9D1	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)
D	V-set_12	e6kn9D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
E	V-set_8	e6kn9E2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E	V-set	e6kn9E1	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)
F	V-set_3	e6kn9F2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
F	V-set_12	e6kn9F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

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
D, E, F	scFv	VH-V-KAPPA	Homo sapiens (human)	IGHV3-6601, IGHV3-6602, IGHV3-6604, IGHJ401, IGHJ402, IGHJ403, IGKV1-3901, IGKV1D-3901, IGKJ1*01	V-DOMAIN VH, V-DOMAIN V-KAPPA	IG	VH-V-KAPPA	IMGT (202414-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF18452	Immunoglobulin domain (Ig_6)	Immunoglobulin domain	This is an immunoglobulin domain which can be found in Interleukin-18 receptor alpha (IL-18Ra). IL-18Ra ectodomain folds into three immunoglobulin (Ig)-like domains, similar to IL-1 receptors. Each domain comprises a two-layer sandwich of six to nin ...	This is an immunoglobulin domain which can be found in Interleukin-18 receptor alpha (IL-18Ra). IL-18Ra ectodomain folds into three immunoglobulin (Ig)-like domains, similar to IL-1 receptors. Each domain comprises a two-layer sandwich of six to nine beta-strands and contains at least one intra-domain disulfide bond [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Interleukin-18 receptor accessory protein	molecular transducer activity coreceptor activity signaling receptor activity hydrolase activity, acting on glycosyl bonds NADP+ nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity NAD+ nucleotidase, cyclic ADP-ribose generating interleukin-18 receptor activity transmembrane signaling receptor activity cytokine receptor activity immune receptor activity	regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of immune effector process lymphocyte mediated immunity positive regulation of leukocyte mediated immunity positive regulation of response to biotic stimulus regulation of cellular process response to stimulus response to biotic stimulus positive regulation of leukocyte mediated cytotoxicity positive regulation of immune response positive regulation of natural killer cell mediated immunity leukocyte mediated immunity regulation of immune system process natural killer cell mediated immunity positive regulation of immune system process regulation of biological process regulation of natural killer cell mediated immunity immune response response to other organism regulation of innate immune response response to external stimulus leukocyte mediated cytotoxicity immune effector process regulation of leukocyte mediated immunity regulation of response to stimulus defense response to other organism positive regulation of defense response natural killer cell mediated cytotoxicity regulation of immune response positive regulation of natural killer cell mediated cytotoxicity regulation of cell killing positive regulation of cell killing regulation of defense response regulation of response to biotic stimulus regulation of natural killer cell mediated cytotoxicity biological process involved in interspecies interaction between organisms regulation of response to external stimulus positive regulation of lymphocyte mediated immunity positive regulation of biological process positive regulation of response to stimulus positive regulation of response to external stimulus response to stress regulation of response to stress innate immune response positive regulation of immune effector process response to external biotic stimulus positive regulation of cellular process positive regulation of innate immune response defense response regulation of leukocyte mediated cytotoxicity biological regulation defense response to symbiont regulation of lymphocyte mediated immunity immune system process cellular process cell killing cellular response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress response to chemical regulation of primary metabolic process regulation of nitrogen compound metabolic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process regulation of cellular metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity aromatic compound biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process positive regulation of DNA-binding transcription factor activity cellular biosynthetic process positive regulation of NF-kappaB transcription factor activity RNA metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process organic substance metabolic process nitrogen compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process cellular aromatic compound metabolic process cell population proliferation neutrophil activation multicellular organismal process cell activation myeloid leukocyte activation granulocyte activation leukocyte activation inflammatory response response to organic substance cell surface receptor signaling pathway signaling cellular response to interleukin-18 response to interleukin-18 response to cytokine cytokine-mediated signaling pathway cell communication interleukin-18-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance signal transduction	cell periphery interleukin-18 receptor complex protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex cellular anatomical entity receptor complex
D, E, F	scFv	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR041416	IL-1Ra-like, immunoglobulin domain	Domain
A, B, C	IPR000157	Toll/interleukin-1 receptor homology (TIR) domain	Domain
A, B, C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B, C	IPR003599	Immunoglobulin subtype	Domain
A, B, C	IPR015621	Interleukin-1 receptor family	Family
A, B, C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B, C	IPR035897	Toll/interleukin-1 receptor homology (TIR) domain superfamily	Homologous Superfamily
A, B, C	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: O95256	ulcerative colitis inflammatory bowel disease Crohn disease psoriasis allergic rhinitis bone disease interstitial cystitis lung cancer nasal cavity disease pancreatic intraductal papillary-mucinous carcinoma asthma celiac disease cutaneous lupus erythematosus leprosy lung carcinoma ulcerative colitis inflammatory bowel disease Crohn disease psoriasis allergic rhinitis bone disease interstitial cystitis lung cancer nasal cavity disease pancreatic intraductal papillary-mucinous carcinoma asthma celiac disease cutaneous lupus erythematosus leprosy lung carcinoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm atopic eczema common variable immunodeficiency lung adenocarcinoma MALT lymphoma 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.