1RF3

Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1rf3a1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 3 (TRAF3)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1rf3a2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1rf3b_	Peptides	Fragments of TNF receptors	Fragments of TNF receptors	Fragments of TNF receptors	Lymphotoxin-beta receptor	( ) [TaxId: ], (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	SCOP2B Superfamily	TRAF domain-like	8040913	3001027	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trimerization domain of TRAF	8040915	3001589	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	MATH	e1rf3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF21355	TRAF/meprin, MATH domain (TRAF-mep_MATH)	TRAF/meprin, MATH domain	Intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the the meprin and TRAF homology (MATH) domain which adopts a beta-sandwich structure. This is the MATH domain of TNF receptor-associated factors (TRAFs) an ...	Intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the the meprin and TRAF homology (MATH) domain which adopts a beta-sandwich structure. This is the MATH domain of TNF receptor-associated factors (TRAFs) and meprins. In TRAFS, it is essential for self-association and receptor interaction [1-3]. Meprins are mammalian tissue-specific metalloendopeptidases involved developmental, normal and pathological processes.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	TNF receptor associated factor 3	thioesterase binding protein binding binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein phosphatase binding thioesterase binding protein binding binding enzyme binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity protein phosphatase binding phosphatase binding kinase binding protein kinase binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding identical protein binding	cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway cellular response to stimulus positive regulation of response to biotic stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus pattern recognition receptor signaling pathway response to biotic stimulus cell communication immune response-activating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cell surface toll-like receptor signaling pathway innate immune response-activating signaling pathway regulation of biological process immune response response to other organism immune response-activating cell surface receptor signaling pathway regulation of innate immune response response to external stimulus regulation of response to stimulus defense response to other organism positive regulation of defense response activation of innate immune response regulation of immune response activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus signaling positive regulation of biological process innate immune response activating cell surface receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus cell surface pattern recognition receptor signaling pathway positive regulation of innate immune response cell surface receptor signaling pathway defense response biological regulation defense response to symbiont immune system process toll-like receptor 4 signaling pathway cellular process organonitrogen compound metabolic process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of nitrogen compound metabolic process organic substance metabolic process regulation of proteolysis proteolysis nitrogen compound metabolic process metabolic process protein metabolic process macromolecule metabolic process regulation of metabolic process apoptotic process cell death programmed cell death regulation of apoptotic process regulation of programmed cell death Toll signaling pathway multicellular organismal process cellular biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production regulation of multicellular organismal process regulation of interferon-beta production interferon-beta production regulation of biosynthetic process type I interferon production cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of type I interferon production toll-like receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway nucleobase-containing compound metabolic process negative regulation of NF-kappaB transcription factor activity DNA-templated transcription regulation of RNA metabolic process heterocycle metabolic process regulation of nucleobase-containing compound metabolic process cellular nitrogen compound metabolic process regulation of molecular function organic cyclic compound metabolic process regulation of DNA-binding transcription factor activity aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription negative regulation of DNA-binding transcription factor activity RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process regulation of RNA biosynthetic process negative regulation of molecular function nucleobase-containing compound biosynthetic process heterocycle biosynthetic process nucleic acid metabolic process cellular aromatic compound metabolic process regulation of defense response to virus defense response to virus response to virus protein polyubiquitination protein K63-linked ubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal response to organic substance response to cytokine cytokine-mediated signaling pathway cellular response to chemical stimulus cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance response to tumor necrosis factor positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process positive regulation of type I interferon production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of cellular biosynthetic process regulation of signaling regulation of signal transduction intracellular signal transduction canonical NF-kappaB signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of cell communication regulation of canonical NF-kappaB signal transduction interferon-mediated signaling pathway cellular response to type I interferon type I interferon-mediated signaling pathway response to type I interferon	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle cell periphery protein-containing complex plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex cytosol endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle protein kinase complex transferase complex, transferring phosphorus-containing groups catalytic complex serine/threonine protein kinase complex transferase complex endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane ubiquitin ligase complex intracellular protein-containing complex
B	24-residue peptide from Lymphotoxin-B Receptor	ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus developmental process immune system development multicellular organism development multicellular organismal process immune system process animal organ development anatomical structure development hematopoietic or lymphoid organ development system development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process positive regulation of signaling positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction myeloid leukocyte differentiation cellular developmental process myeloid dendritic cell activation hemopoiesis cell activation cell development mononuclear cell differentiation myeloid leukocyte activation leukocyte activation myeloid cell differentiation cell differentiation myeloid dendritic cell differentiation dendritic cell differentiation leukocyte differentiation response to mechanical stimulus response to external 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 immune response apoptotic process cell death programmed cell death regulation of programmed cell death extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death cell surface receptor signaling pathway regulation of apoptotic process positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway	membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012227	TNF receptor-associated factor TRAF, metazoa	Family
A	IPR001293	Zinc finger, TRAF-type	Domain
A	IPR002083	MATH/TRAF domain	Domain
A	IPR049342	TRAF1-6/MEP1A/B-like, MATH domain	Domain
A	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A	IPR027128	TNF receptor-associated factor 3, C3HC3D-type RING zinc finger	Domain
A	IPR049440	TNF receptor-associated factor 3/5, RING domain	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR037304	TNF receptor-associated factor 3, MATH domain	Domain
A	IPR001841	Zinc finger, RING-type	Domain
A	IPR008974	TRAF-like	Homologous Superfamily
B	IPR017349	Tumour necrosis factor receptor 3	Family
B	IPR001368	TNFR/NGFR cysteine-rich region	Domain
B	IPR033997	Tumour necrosis factor receptor 3, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q13114	herpes simplex encephalitis, susceptibility to, 3 allergic rhinitis glioblastoma herpes simplex encephalitis, susceptibility to, 1 Herpetic meningoencephalitis medulloblastoma psoriasis tuberculosis attention deficit hyperactivity disorder, inattentive type lung cancer osteosarcoma Sjogren syndrome gastric carcinoma herpes simplex encephalitis malignant glioma herpes simplex encephalitis, susceptibility to, 3 allergic rhinitis glioblastoma herpes simplex encephalitis, susceptibility to, 1 Herpetic meningoencephalitis medulloblastoma psoriasis tuberculosis attention deficit hyperactivity disorder, inattentive type lung cancer osteosarcoma Sjogren syndrome gastric carcinoma herpes simplex encephalitis malignant glioma ovarian cancer subependymal giant cell astrocytoma
B	Pharos: P36941	malaria ankylosing spondylitis colorectal cancer psoriasis celiac disease Crohn disease ovarian cancer subependymal giant cell astrocytoma colorectal adenoma juvenile idiopathic arthritis primary biliary cholangitis tuberculosis

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.