1TNR

CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN 55 KD TNF RECEPTOR-HUMAN TNF-BETA COMPLEX: IMPLICATIONS FOR TNF RECEPTOR ACTIVATION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d1tnra_	All beta proteins	TNF-like	TNF-like	TNF-like	Tumor necrosis factor (TNF)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth R]	d1tnrr3	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Tumor necrosis factor (TNF) receptor, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth R]	d1tnrr2	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Tumor necrosis factor (TNF) receptor, middle domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth R]	d1tnrr1	Small proteins	TNF receptor-like	TNF receptor-like	TNF receptor-like	Tumor necrosis factor (TNF) receptor, N-terminal domain	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	SCOP2 Family	TNF-like	8064726	4000294	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TNF-like	8064727	3000061	SCOP2 (2022-06-29)
B [auth R]	SCOP2B Superfamily	TNF receptor-like	8038880	3000971	SCOP2B (2022-06-29)
B [auth R]	SCOP2B Superfamily	TNF receptor-like	8038879	3000971	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	TNF	e1tnrA1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: TNF	ECOD (1.6)
B [auth R]	TNFR_c6_2	e1tnrR2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_2	ECOD (1.6)
B [auth R]	TNFR_c6_1	e1tnrR3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: TNFR_c6_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B [auth R]	2.10.50.10	Mainly Beta	Ribbon	Tumor Necrosis Factor Receptor, subunit A	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain
B [auth R]	PF00020	TNFR/NGFR cysteine-rich region (TNFR_c6)	TNFR/NGFR cysteine-rich region	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	TUMOR NECROSIS FACTOR BETA	protein binding binding signaling receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development humoral immune response response to stimulus response to chemical response to xenobiotic stimulus developmental process immune system development multicellular organism development multicellular organismal process lymph node development immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development humoral immune response immune response positive regulation of chronic inflammatory response regulation of defense response chronic inflammatory response regulation of response to external stimulus positive regulation of biological process regulation of chronic inflammatory response to antigenic stimulus inflammatory response to antigenic stimulus positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response positive regulation of immune response response to stress regulation of response to stress regulation of immune system process positive regulation of chronic inflammatory response to antigenic stimulus positive regulation of immune system process regulation of biological process regulation of chronic inflammatory response defense response regulation of inflammatory response to antigenic stimulus chronic inflammatory response to antigenic stimulus biological regulation response to external stimulus regulation of inflammatory response positive regulation of inflammatory response to antigenic stimulus regulation of response to stimulus positive regulation of defense response regulation of immune response inflammatory response cellular process apoptotic process cell death programmed cell death positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of cellular process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of humoral immune response lymphocyte mediated immunity regulation of immune effector process 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 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 regulation of immunoglobulin mediated immune response leukocyte mediated immunity positive regulation of immune effector process positive regulation of adaptive immune response 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 adaptive immune response regulation of B cell mediated immunity immune effector process regulation of leukocyte mediated immunity regulation of lymphocyte mediated immunity B cell mediated immunity signaling cell-cell signaling cell communication cellular response to stimulus signal transduction negative regulation of cell population proliferation fibroblast proliferation cell population proliferation negative regulation of biological process regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of fibroblast proliferation response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of nervous system development cellular developmental process regulation of developmental process positive regulation of cell population proliferation cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis positive regulation of glial cell proliferation positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis regulation of glial cell proliferation gliogenesis positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis regulation of multicellular organismal development positive regulation of cell development nervous system development positive regulation of multicellular organismal process glial cell proliferation response to nutrient levels response to nutrient response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism response to oxygen-containing compound response to lipopolysaccharide response to biotic stimulus response to bacterium response to external biotic stimulus response to molecule of bacterial origin regulation of type II interferon production type II interferon production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of type II interferon production regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process defense response to Gram-positive bacterium defense response to bacterium defense response to other organism	cell periphery plasma membrane membrane cellular anatomical entity extracellular region extracellular space
B [auth R]	TUMOR NECROSIS FACTOR RECEPTOR P55	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity tumor necrosis factor receptor activity death receptor activity protein binding binding cytokine binding tumor necrosis factor binding	cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular process cellular response to organic substance signal transduction positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling regulation of defense response regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response regulation of lipid metabolic process primary metabolic process regulation of primary metabolic process positive regulation of metabolic process organic substance metabolic process positive regulation of lipid metabolic process metabolic process regulation of metabolic process lipid metabolic process cellular biosynthetic process cellular metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process macromolecule metabolic process negative regulation of extracellular matrix organization regulation of localization regulation of cellular component organization transport negative regulation of biological process extracellular matrix organization negative regulation of transport cellular component organization localization negative regulation of secretion regulation of secretion by cell secretion by cell negative regulation of cellular process negative regulation of secretion by cell cellular component organization or biogenesis regulation of extracellular matrix constituent secretion extracellular structure organization negative regulation of cellular component organization regulation of transport secretion export from cell establishment of localization regulation of secretion negative regulation of extracellular matrix constituent secretion extracellular matrix constituent secretion regulation of extracellular matrix organization external encapsulating structure organization negative regulation of inflammatory response negative regulation of response to stimulus negative regulation of response to external stimulus negative regulation of defense response regulation of amide metabolic process positive regulation of amide metabolic process amide metabolic process prostaglandin metabolic process icosanoid metabolic process fatty acid metabolic process unsaturated fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process prostanoid metabolic process cellular lipid metabolic process small molecule metabolic process monocarboxylic acid metabolic process protein localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane biological process involved in interspecies interaction between organisms response to other organism response to biotic stimulus defense response to bacterium defense response to other organism response to bacterium response to external biotic stimulus positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis apoptotic process programmed cell death developmental process heart development multicellular organismal process heart valve development animal organ development circulatory system development multicellular organism development pulmonary valve development anatomical structure development semi-lunar valve development system development extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway cellular response to stress DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway response to mechanical stimulus response to abiotic stimulus cellular response to mechanical stimulus cellular response to abiotic stimulus cellular response to external stimulus cellular response to environmental stimulus positive regulation of phosphorylation positive regulation of phosphate metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation tyrosine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of cellular metabolic process macromolecule modification regulation of phosphorus metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process protein metabolic process organonitrogen compound metabolic process regulation of tyrosine phosphorylation of STAT protein regulation of peptidyl-tyrosine phosphorylation regulation of macromolecule metabolic process positive regulation of tyrosine phosphorylation of STAT protein regulation of phosphorylation peptidyl-tyrosine phosphorylation cell surface receptor signaling pathway via JAK-STAT membrane lipid metabolic process regulation of membrane lipid metabolic process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process endothelium development cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development cell differentiation regulation of endothelial cell development regulation of multicellular organismal process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation tissue development epithelial cell development establishment of endothelial barrier cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway response to tumor necrosis factor apoptotic process involved in morphogenesis apoptotic process involved in development positive regulation of developmental process positive regulation of apoptotic process involved in morphogenesis positive regulation of apoptotic process involved in development regulation of apoptotic process involved in development anatomical structure morphogenesis regulation of apoptotic process involved in morphogenesis aortic valve development muscle hypertrophy regulation of muscle adaptation system process negative regulation of muscle hypertrophy regulation of system process striated muscle hypertrophy regulation of muscle system process muscle system process regulation of muscle hypertrophy regulation of cardiac muscle hypertrophy muscle adaptation cardiac muscle hypertrophy negative regulation of multicellular organismal process negative regulation of cardiac muscle hypertrophy regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of response to cytokine stimulus positive regulation of macromolecule biosynthetic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane cellular anatomical entity cell surface cell periphery plasma membrane membrane microdomain membrane raft protein-containing complex receptor complex extracellular region membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane cellular anatomical entity cell surface cell periphery plasma membrane membrane microdomain membrane raft protein-containing complex receptor complex extracellular region membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle organelle cytoplasm organelle membrane tumor necrosis factor receptor superfamily complex extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A	IPR006052	Tumour necrosis factor domain	Domain
A	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
A	IPR006053	Tumour necrosis factor	Family
A	IPR002960	Lymphotoxin-alpha	Family
B [auth R]	IPR033993	Tumor necrosis factor receptor 1A, N-terminal	Domain
B [auth R]	IPR011029	Death-like domain superfamily	Homologous Superfamily
B [auth R]	IPR020419	Tumour necrosis factor receptor 1A	Family
B [auth R]	IPR000488	Death domain	Domain
B [auth R]	IPR001368	TNFR/NGFR cysteine-rich region	Domain
B [auth R]	IPR033994	Tumor necrosis factor receptor 1A, death domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P01374	psoriatic arthritis hepatic encephalopathy leprosy malignant mesothelioma myocardial infarction coronary artery disease Sepsis psoriasis Crohn disease esophageal squamous cell carcinoma hepatic coma hypertensive disorder liver disease major depressive disorder metabolic syndrome X psoriatic arthritis hepatic encephalopathy leprosy malignant mesothelioma myocardial infarction coronary artery disease Sepsis psoriasis Crohn disease esophageal squamous cell carcinoma hepatic coma hypertensive disorder liver disease major depressive disorder metabolic syndrome X AIDS peripheral nervous system disease cancer schizophrenia cutaneous lupus erythematosus ulcerative colitis HIV infectious disease laryngeal squamous cell carcinoma lung adenocarcinoma alopecia areata peripheral neuropathy carpal tunnel syndrome Dengue hemorrhagic fever squamous cell lung carcinoma Hashimoto thyroiditis Hodgkins lymphoma lung carcinoma membranous glomerulonephritis myositis autism spectrum disorder cervical cancer rheumatoid arthritis Stevens-Johnson syndrome herpes zoster
B [auth R]	Pharos: P19438	autosomal dominant familial periodic fever primary biliary cholangitis multiple sclerosis cystic fibrosis congestive heart failure autoimmune disease Diabetes Mellitus, Experimental amyloidosis allergic disease type 2 diabetes mellitus brain ischemia pneumonia celiac disease malignant ependymoma colorectal adenoma autosomal dominant familial periodic fever primary biliary cholangitis multiple sclerosis cystic fibrosis congestive heart failure autoimmune disease Diabetes Mellitus, Experimental amyloidosis allergic disease type 2 diabetes mellitus brain ischemia pneumonia celiac disease malignant ependymoma colorectal adenoma medulloblastoma Crohn disease ovarian cancer pilocytic astrocytoma acquired metabolic disease pneumonitis heart failure schizophrenia arthritic joint disease intermittent hydrarthrosis brain injury lung carcinoma malignant pancreatic neoplasm colorectal cancer multiple sclerosis, susceptibility to, 5 pancreatic ductal adenocarcinoma pituitary cancer glioblastoma ankylosing spondylitis astrocytic tumor Behcet disease juvenile idiopathic arthritis cancer maturity-onset diabetes of the young depressive disorder exocrine pancreatic carcinoma periodic fever syndrome hepatocellular carcinoma subependymal giant cell astrocytoma large cell medulloblastoma lung cancer

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.