3X1O

Crystal structure of the ROQ domain of human Roquin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	KOG3161_2nd	e3x1oA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KOG3161_2nd	ECOD (1.6)
A	KOG3161_1st	e3x1oA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG3161_1st	ECOD (1.6)
B	KOG3161_2nd	e3x1oB2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: KOG3161_2nd	ECOD (1.6)
B	KOG3161_1st	e3x1oB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: KOG3161_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.1790	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)
B	1.20.120.1790	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18386	Roquin II domain (ROQ_II)	Roquin II domain	The ROQ domain is composed of three subdomains, I, II and III. This entry describes the second domain, ROQ II. Structural analysis reveals similarity of domain II to the helix-turn-helix (HTH) fold. Mutagenesis and biochemical studies show that that ...	The ROQ domain is composed of three subdomains, I, II and III. This entry describes the second domain, ROQ II. Structural analysis reveals similarity of domain II to the helix-turn-helix (HTH) fold. Mutagenesis and biochemical studies show that that the HTH fold in domain II contributes to binding dsRNA at the 5'arm [1].	Domain
A, B	PF21206	Roquin 1/2-like, ROQ domain (Roquin_1_2-like_ROQ)	Roquin 1/2-like, ROQ domain	This domain is found in Roquin-1/2 from humans and in other eukaryotic RING-E3 ubiquitin ligases and transferases. These paralogous proteins Roquin-1/2 recruit the deadenylation and decapping machineries to initiate mRNA degradation. They play a cent ...	This domain is found in Roquin-1/2 from humans and in other eukaryotic RING-E3 ubiquitin ligases and transferases. These paralogous proteins Roquin-1/2 recruit the deadenylation and decapping machineries to initiate mRNA degradation. They play a central role in repressing autoimmunity. The ROQ domain, highly conserved, is required for RNA binding and shows a mostly helical structure with a small three-stranded beta-sheet. It bears a winged helix-turn-helix motif, which is involved in the binding of constitutive decay elements-containing stem-loop mRNAs [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Roquin-1	RNA binding double-stranded RNA binding binding nucleic acid binding mRNA 3'-UTR binding mRNA binding regulatory RNA binding miRNA 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 RNA binding double-stranded RNA binding binding nucleic acid binding mRNA 3'-UTR binding mRNA binding regulatory RNA binding miRNA 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-containing complex binding CCR4-NOT complex binding RNA stem-loop binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process negative regulation of lymphocyte proliferation multicellular organismal process regulation of leukocyte activation regulation of cell activation lymphocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte activation negative regulation of mononuclear cell proliferation negative regulation of leukocyte proliferation regulation of B cell proliferation lymphocyte proliferation regulation of B cell activation regulation of immune system process regulation of multicellular organismal process negative regulation of B cell activation regulation of lymphocyte proliferation regulation of leukocyte proliferation negative regulation of cell population proliferation cell population proliferation B cell activation cell activation B cell proliferation negative regulation of B cell proliferation negative regulation of cell activation negative regulation of immune system process regulation of cell population proliferation mononuclear cell proliferation immune system process regulation of mononuclear cell proliferation negative regulation of multicellular organismal process negative regulation of leukocyte activation regulation of lymphocyte activation regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of mRNA catabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality regulation of catabolic process regulation of mRNA stability regulation of RNA stability regulation of mRNA metabolic process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response signal transduction positive regulation of immune system process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response T cell receptor signaling pathway regulation of response to stimulus regulation of immune response antigen receptor-mediated signaling pathway activation of immune response developmental process immune system development multicellular organism development lymph node development animal organ development anatomical structure development hematopoietic or lymphoid organ development system development negative regulation of T cell proliferation negative regulation of cell adhesion T cell activation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion regulation of activated T cell proliferation leukocyte cell-cell adhesion activated T cell proliferation cell adhesion cell-cell adhesion regulation of cell-cell adhesion T cell proliferation regulation of cell adhesion regulation of T cell activation regulation of T cell proliferation negative regulation of activated T cell proliferation regulation of immune effector process regulation of leukocyte differentiation regulation of alpha-beta T cell activation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response alpha-beta T cell differentiation involved in immune response regulation of cell development negative regulation of T cell differentiation cell differentiation regulation of T-helper cell differentiation alpha-beta T cell activation T cell differentiation negative regulation of hemopoiesis T-helper cell differentiation negative regulation of leukocyte differentiation negative regulation of immune response negative regulation of immune effector process immune effector process negative regulation of CD4-positive, alpha-beta T cell activation negative regulation of lymphocyte differentiation negative regulation of CD4-positive, alpha-beta T cell differentiation leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation CD4-positive, alpha-beta T cell differentiation negative regulation of alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response alpha-beta T cell activation involved in immune response CD4-positive, alpha-beta T cell activation leukocyte activation involved in immune response negative regulation of cell differentiation lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of response to stimulus hemopoiesis negative regulation of developmental process T cell differentiation involved in immune response negative regulation of T-helper cell differentiation negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation regulation of hemopoiesis negative regulation of alpha-beta T cell activation regulation of antigen receptor-mediated signaling pathway regulation of signal transduction regulation of signaling regulation of T cell receptor signaling pathway regulation of cell communication multicellular organismal-level homeostasis leukocyte homeostasis T cell homeostasis homeostatic process homeostasis of number of cells lymphocyte homeostasis 3'-UTR-mediated mRNA destabilization positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process mRNA destabilization positive regulation of cellular process RNA destabilization positive regulation of catabolic process positive regulation of mRNA catabolic process B cell homeostasis cellular component biogenesis cellular component organization organelle organization cellular component assembly organelle assembly P-body assembly membraneless organelle assembly cellular component organization or biogenesis adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of germinal center formation regulation of adaptive immune response adaptive immune response anatomical structure morphogenesis regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains anatomical structure formation involved in morphogenesis germinal center formation regulation of anatomical structure morphogenesis nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay proteolysis involved in protein catabolic process protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process protein metabolic process spleen development protein polyubiquitination 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 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling regulation of miRNA metabolic process miRNA metabolic process T follicular helper cell differentiation nuclear-transcribed mRNA catabolic process, nonsense-mediated decay negative regulation of adaptive immune response negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains negative regulation of germinal center formation response to peptide cellular response to interleukin-1 response to chemical response to cytokine cellular response to cytokine stimulus response to interleukin-1 T-helper 17 cell differentiation negative regulation of T-helper 17 cell differentiation regulation of T-helper 17 cell differentiation negative regulation of T-helper 17 type immune response regulation of T-helper 17 type immune response T-helper 17 type immune response	intracellular anatomical structure cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule intracellular organelle cellular anatomical structure organelle membraneless organelle cytoplasm supramolecular complex cytoplasmic stress granule P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR052249	Roquin domain-containing protein	Family
A, B	IPR036855	Zinc finger, CCCH-type superfamily	Homologous Superfamily
A, B	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B	IPR000571	Zinc finger, CCCH-type	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR041523	Roquin II	Domain
A, B	IPR048575	Roquin 1/2-like, ROQ domain	Domain
A, B	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q5TC82	atypical teratoid rhabdoid tumor cystic fibrosis ovarian cancer pancreatic intraductal papillary-mucinous neoplasm spina bifida bipolar disorder malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia breast cancer medulloblastoma pancreatic intraductal papillary-mucinous carcinoma Sjogren syndrome

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.