1D0J

STRUCTURE OF TNF RECEPTOR ASSOCIATED FACTOR 2 IN COMPLEX WITH A M4-1BB PEPTIDE

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1d0ja1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1d0ja2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1d0jb1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1d0jb2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1d0jc1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1d0jc2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1d0jd1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1d0jd2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1d0je1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d1d0je2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1d0jf1	All beta proteins	TRAF domain-like	TRAF domain-like	MATH domain	TNF receptor associated factor 2 (TRAF2)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d1d0jf2	Coiled coil proteins	Parallel coiled-coil	Trimerization domain of TRAF	Trimerization domain of TRAF	TRAF2	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	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	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	e1d0jA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)
B	MATH	e1d0jB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)
C	MATH	e1d0jC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)
D	MATH	e1d0jD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)
E	MATH	e1d0jE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: TRAF domain-like (From Topology)	T: TRAF domain-like	F: MATH	ECOD (1.6)
F	MATH	e1d0jF1	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)
B	2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2	Chain A	CATH (4.3.0)
C	2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2	Chain A	CATH (4.3.0)
D	2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2	Chain A	CATH (4.3.0)
E	2.60.210.10	Mainly Beta	Sandwich	Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2	Chain A	CATH (4.3.0)
F	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, B, C, D, E A, B, C, D, E, F	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, B, C, D, E A, B, C, D, E, F	TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED PROTEIN 2	binding sphingolipid binding lipid binding thioesterase binding protein 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 binding sphingolipid binding lipid binding thioesterase binding protein 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-macromolecule adaptor activity molecular adaptor activity protein phosphatase binding phosphatase binding protein-containing complex binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding kinase binding mitogen-activated protein kinase kinase kinase binding protein kinase binding identical protein binding signaling adaptor activity signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding CD40 receptor binding cytokine binding tumor necrosis factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding tumor necrosis factor receptor binding	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 response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor 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 response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication cellular process response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling regulation of JNK cascade regulation of MAPK cascade intracellular signal transduction regulation of intracellular signal transduction JNK cascade intracellular signaling cassette MAPK cascade adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains multicellular organismal process regulation of immune effector process lymphocyte mediated immunity T cell mediated immunity positive regulation of leukocyte mediated immunity T cell cytokine production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of immune response cytokine production leukocyte mediated immunity regulation of immune system process positive regulation of macromolecule metabolic process positive regulation of adaptive immune response positive regulation of T cell cytokine production positive regulation of immune system process regulation of T cell mediated immunity regulation of cytokine production involved in immune response immune response regulation of adaptive immune response immune effector process regulation of gene expression regulation of leukocyte mediated immunity biosynthetic process positive regulation of production of molecular mediator of immune response positive regulation of multicellular organismal process regulation of immune response metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of production of molecular mediator of immune response positive regulation of cytokine production regulation of metabolic process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity regulation of T cell cytokine production regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of biosynthetic process regulation of cytokine production positive regulation of immune effector process regulation of multicellular organismal process cytokine production involved in immune response production of molecular mediator of immune response regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process adaptive immune response regulation of lymphocyte mediated immunity positive regulation of gene expression immune system process positive regulation of T cell mediated immunity positive regulation of cytokine production involved in immune response positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus protein autoubiquitination protein ubiquitination macromolecule modification protein metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process protein catabolic process macromolecule catabolic process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to interleukin-17 response to interleukin-17 interleukin-17-mediated signaling pathway non-canonical NF-kappaB signal transduction CD40 signaling pathway positive regulation of NF-kappaB transcription factor activity signal transduction involved in regulation of gene expression regulation of glial cell apoptotic process negative regulation of programmed cell death negative regulation of biological process negative regulation of glial cell apoptotic process glial cell apoptotic process negative regulation of apoptotic process negative regulation of cellular process positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity regulation of phosphate metabolic process phosphate-containing compound metabolic process phosphorus metabolic process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation positive regulation of MAPK cascade regulation of protein metabolic process positive regulation of intracellular signal transduction positive regulation of JUN kinase activity positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of JUN kinase activity regulation of phosphorylation cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to nitric oxide cellular response to chemical stimulus response to nitric oxide cellular response to reactive nitrogen species cellular response to stress response to endoplasmic reticulum stress regulation of cellular component organization protein-containing complex organization regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly cellular component organization or biogenesis positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction extrinsic apoptotic signaling pathway positive regulation of apoptotic signaling pathway positive regulation of programmed cell death 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 post-transcriptional regulation of gene expression negative regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA stabilization mRNA catabolic process negative regulation of metabolic process nucleobase-containing compound catabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process negative regulation of RNA metabolic process negative regulation of mRNA metabolic process regulation of mRNA catabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of mRNA catabolic process negative regulation of RNA catabolic process regulation of catabolic process mRNA metabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process protein polyubiquitination protein K63-linked ubiquitination immunoglobulin production regulation of immunoglobulin production programmed necrotic cell death regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress intrinsic apoptotic signaling pathway	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex CD40 receptor complex receptor complex membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle IRE1-TRAF2-ASK1 complex organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane cytosol vesicle membrane vesicle tumor necrosis factor receptor superfamily complex ubiquitin ligase complex catalytic complex transferase complex intracellular protein-containing complex cell cortex membrane microdomain membrane raft nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen TRAF2-GSTP1 complex cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane
G, H, I, J, K	4-1BB LIGAND RECEPTOR	molecular transducer activity signaling receptor activity	cellular process apoptotic process cell death programmed cell death negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process multicellular organismal process cellular developmental process cellular process apoptotic process cell death programmed cell death negative regulation of cell population proliferation regulation of biological process cell population proliferation regulation of cellular process regulation of cell population proliferation negative regulation of cellular process biological regulation negative regulation of biological process multicellular organismal process cellular developmental process regulation of leukocyte activation immature T cell proliferation in thymus regulation of cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte proliferation leukocyte activation T cell differentiation in thymus T cell activation cell differentiation lymphocyte proliferation anatomical structure development regulation of immature T cell proliferation regulation of multicellular organismal process regulation of immune system process T cell differentiation T cell proliferation regulation of lymphocyte proliferation developmental process regulation of leukocyte proliferation hemopoiesis cell activation regulation of T cell activation immature T cell proliferation regulation of immature T cell proliferation in thymus regulation of T cell proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation leukocyte differentiation	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR012227	TNF receptor-associated factor TRAF, metazoa	Family
A, B, C, D, E A, B, C, D, E, F	IPR001293	Zinc finger, TRAF-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032070	TNF receptor-associated factor, BIRC3 binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001841	Zinc finger, RING-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008974	TRAF-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR049441	TRAF2, second zinc finger	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002083	MATH/TRAF domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR018957	Zinc finger, C3HC4 RING-type	Domain
A, B, C, D, E A, B, C, D, E, F	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR049342	TRAF1-6, MATH domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR027133	TNF receptor-associated factor 2, C3HC3D-type RING zinc finger	Domain
A, B, C, D, E A, B, C, D, E, F	IPR037305	TNF receptor-associated factor 2, MATH domain	Domain
G, H, I, J, K	IPR001368	TNFR/NGFR cysteine-rich region	Domain
G, H, I, J, K	IPR020413	Tumour necrosis factor receptor 9	Family
G, H, I, J, K	IPR034020	Tumour necrosis factor receptor 9, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: Q12933	malignant mesothelioma psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I, J, K	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.