Annotations: 8T5Q

SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	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)
D	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TRAF domain-like	8040736	3001027	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trimerization domain of TRAF	8039390	3001589	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	MFS_1	e8t5qF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: MFS_1	ECOD (v295)
E	MFS_1	e8t5qE1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: MFS_1	ECOD (v295)
D	MFS_1	e8t5qD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: MFS_1	ECOD (v295)
C	MFS_1	e8t5qC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: MFS_1	ECOD (v295)
B	MFS_1	e8t5qB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: MFS_1	ECOD (v295)
A	tRNA-synt_His	e8t5qA01	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: tRNA-synt_His	ECOD (v295)

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
G, H, I	ORF3a protein	molecular function activator activity molecular function regulator activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity identical protein binding protein binding binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process symbiont-mediated activation of host reticulophagy symbiont-mediated perturbation of host autophagy modulation of process of another organism symbiont-mediated activation of host autophagy biological process involved in interaction with host biological process involved in symbiotic interaction	virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region virion component virion membrane cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host intracellular region host cell lysosome host cell endosome cell periphery plasma membrane membrane host cell membrane host cell endomembrane system host cell endoplasmic reticulum membrane host cell plasma membrane cytoplasmic side of plasma membrane cytoplasmic side of membrane side of membrane
A, B, C, D, E A, B, C, D, E, F	TNF receptor-associated factor 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 protein autoubiquitination primary metabolic process 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 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 extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway CD40 signaling pathway 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 regulation of primary metabolic process positive regulation of protein serine/threonine kinase activity phosphate-containing compound metabolic process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation phosphorylation positive regulation of MAPK cascade regulation of protein metabolic process positive regulation of intracellular signal transduction positive regulation of JUN kinase activity regulation of molecular function positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of protein kinase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of JUN kinase activity regulation of phosphorylation cellular response to stress 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 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 regulation of apoptotic signaling pathway nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process negative regulation of nucleobase-containing compound metabolic process 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 catabolic process RNA metabolic process macromolecule catabolic 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 nucleic acid metabolic process regulation of mRNA stability RNA stabilization negative regulation of biosynthetic process regulation of RNA stability regulation of mRNA metabolic process T cell activation cell activation lymphocyte activation leukocyte activation DNA damage response intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway protein polyubiquitination protein K63-linked ubiquitination CD27 signaling pathway cellular component disassembly protein-containing complex disassembly TORC2 complex disassembly regulation of interleukin-2 production interleukin-2 production positive regulation of interleukin-2 production regulation of defense response regulation of response to external stimulus defense response pyroptotic inflammatory 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 positive regulation of defense response positive regulation of pyroptotic inflammatory response inflammatory response intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress TORC1 complex assembly positive regulation of response to biotic stimulus regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms pattern recognition receptor signaling pathway toll-like receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway immune response-regulating signaling pathway innate immune response response to external biotic stimulus innate immune response-activating signaling pathway positive regulation of innate immune response response to other organism regulation of innate immune response defense response to symbiont defense response to other organism activation of innate immune response activation of immune response	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane plasma membrane signaling receptor complex membrane protein complex signaling receptor complex CD40 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 signaling receptor complex CD40 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I	IPR046446	3a-like viroporin, cytosolic domain, alpha/betacoronavirus	Domain
G, H, I	IPR024407	Protein 3a, betacoronavirus	Family
G, H, I	IPR046445	3a-like viroporin, transmembrane domain, alpha/betacoronavirus	Domain
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

Pharos: Disease Associations Pharos Homepage Annotation

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.