5H9W

Crystal structure of Regnase PIN domain, form II

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PIN domain-like	8105559	3001041	SCOP2B (2022-06-29)
B	SCOP2 Family	Zc3h12a NYN domain-like	8047183	4005493	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PIN domain-like	8105559	3001041	SCOP2 (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	RNase_Zc3h12a	e5h9wA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: RNase_Zc3h12a	ECOD (1.6)
B	RNase_Zc3h12a	e5h9wB1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: PIN domain-like	F: RNase_Zc3h12a	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.11980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.11980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11977	Zc3h12a-like Ribonuclease NYN domain (RNase_Zc3h12a)	Zc3h12a-like Ribonuclease NYN domain	This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also be ...	This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes [1]. It has been suggested that this domain belongs to the PIN domain superfamily [1]. This domain has also been identified as part of the NYN domain family [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Ribonuclease ZC3H12A	nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity mRNA 3'-UTR binding RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding DNA binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity mRNA 3'-UTR binding RNA binding binding organic cyclic compound binding nucleic acid binding mRNA binding DNA binding catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity exonuclease activity endonuclease activity RNA endonuclease activity RNA stem-loop binding cation binding ion binding metal ion binding small molecule binding chromatin binding mRNA 3'-UTR AU-rich region binding regulatory RNA binding miRNA binding cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein deubiquitinase activity ribonucleoprotein complex binding protein-containing complex binding ribosome binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis multicellular organismal process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process cellular response to arsenic-containing substance response to sodium arsenite response to arsenic-containing substance cellular response to chemical stimulus response to chemical cellular response to salt cellular response to sodium arsenite response to salt response to peptide response to chemokine response to cytokine cellular response to cytokine stimulus cellular response to chemokine interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production positive regulation of biological process 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 gene expression positive regulation of cellular biosynthetic process cellular response to nutrient levels response to nutrient levels response to starvation cellular response to glucose starvation cellular response to starvation apoptotic process cell death programmed cell death catabolic process RNA metabolic process primary metabolic process miRNA catabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process nucleic acid catabolic process miRNA metabolic process RNA catabolic process regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation 3'-UTR-mediated mRNA destabilization post-transcriptional regulation of gene expression regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process mRNA metabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis positive regulation of miRNA metabolic process regulation of miRNA metabolic process regulation of miRNA catabolic process positive regulation of miRNA catabolic process protein localization regulation of localization cellular localization establishment of protein localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport positive regulation of nucleocytoplasmic transport nuclear transport positive regulation of establishment of protein localization regulation of protein localization to nucleus positive regulation of protein transport localization import into nucleus regulation of protein import into nucleus cellular macromolecule localization establishment of localization in cell protein import into nucleus positive regulation of intracellular transport regulation of intracellular transport regulation of transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus regulation of protein transport establishment of localization positive regulation of transport establishment of protein localization to organelle regulation of cellular localization protein transport macromolecule localization protein localization to organelle positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport response to oxidative stress cellular response to oxidative stress cellular response to chemical stress developmental process multicellular organism development anatomical structure development nervous system development system development regulation of type II interferon production type II interferon production negative regulation of type II interferon production regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus regulation of defense response to virus defense response to virus regulation of response to stimulus defense response to other organism regulation of response to stress positive regulation of defense response to virus by host regulation of defense response to virus by host response to external biotic stimulus response to virus protein deubiquitination protein modification by small protein removal post-translational protein modification protein modification by small protein conjugation or removal response to lipid cellular response to ionomycin response to fatty acid cellular response to organic cyclic compound response to oxygen-containing compound cellular response to ether cellular response to oxygen-containing compound cellular response to fatty acid response to ether cellular response to lipid response to ionomycin response to organic cyclic compound fat cell differentiation positive regulation of fat cell differentiation regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation regulation of fat cell differentiation positive regulation of DNA-templated transcription RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to interleukin-1 response to interleukin-1 positive regulation of autophagy autophagy regulation of autophagy cellular catabolic process regulation of cellular catabolic process positive regulation of cellular catabolic process process utilizing autophagic mechanism negative regulation by host of viral genome replication modulation by host of symbiont process viral life cycle negative regulation by host of viral process modulation by host of viral genome replication biological process involved in symbiotic interaction modulation by host of viral process viral genome replication viral process biological process involved in interaction with symbiont immune response-regulating cell surface receptor signaling pathway signaling cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process 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 immune system process regulation of immune response antigen receptor-mediated signaling pathway activation of immune response positive regulation of locomotion regulation of cell motility endothelial cell migration positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cell motility locomotion blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development anatomical structure morphogenesis tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction canonical NF-kappaB signal transduction regulation of cell communication regulation of canonical NF-kappaB signal transduction lipid storage lipid localization positive regulation of lipid localization maintenance of location regulation of lipid storage regulation of lipid localization positive regulation of lipid storage interleukin-1 production regulation of interleukin-1 beta production negative regulation of interleukin-1 beta production negative regulation of interleukin-1 production regulation of interleukin-1 production interleukin-1 beta production cellular response to lipopolysaccharide cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to biotic stimulus response to bacterium response to molecule of bacterial origin regulation of nitric oxide biosynthetic process negative regulation of nitric oxide metabolic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process negative regulation of nitric oxide biosynthetic process regulation of nitric oxide metabolic process positive regulation of protein metabolic process positive regulation of post-translational protein modification positive regulation of protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification positive regulation of protein deubiquitination regulation of protein deubiquitination negative regulation of DNA-binding transcription factor activity negative regulation of NF-kappaB transcription factor activity negative regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process cellular response to tumor necrosis factor response to tumor necrosis factor regulation of vasculature development regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of angiogenesis positive regulation of vasculature development regulation of angiogenesis positive regulation of multicellular organismal process positive regulation of cell communication positive regulation of signal transduction p38MAPK cascade positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade positive regulation of p38MAPK cascade regulation of p38MAPK cascade MAPK cascade positive regulation of signaling muscle cell apoptotic process negative regulation of programmed cell death regulation of muscle cell apoptotic process negative regulation of apoptotic process negative regulation of muscle cell apoptotic process inflammatory response regulation of non-canonical NF-kappaB signal transduction negative regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction nuclear-transcribed mRNA catabolic process, nonsense-mediated decay nuclear-transcribed mRNA catabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation alpha-beta T cell differentiation involved in immune response regulation of cell development negative regulation of cell adhesion negative regulation of T cell differentiation T cell activation regulation of T-helper cell differentiation alpha-beta T cell activation T-helper cell differentiation negative regulation of leukocyte differentiation negative regulation of immune effector process immune effector process negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains 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 T-helper 17 cell differentiation cell development negative regulation of T-helper 17 cell differentiation CD4-positive, alpha-beta T cell differentiation regulation of T cell differentiation alpha-beta T cell differentiation T cell activation involved in immune response leukocyte activation involved in immune response regulation of cell-cell adhesion negative regulation of cell differentiation regulation of T-helper 17 cell differentiation hemopoiesis negative regulation of developmental process regulation of cell adhesion cell activation negative regulation of T-helper 17 type immune response negative regulation of cell development regulation of CD4-positive, alpha-beta T cell activation negative regulation of alpha-beta T cell activation regulation of lymphocyte activation regulation of immune effector process regulation of leukocyte differentiation mononuclear cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response T cell differentiation negative regulation of hemopoiesis regulation of adaptive immune response negative regulation of immune response negative regulation of adaptive immune response 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 negative regulation of leukocyte activation leukocyte differentiation regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation lymphocyte activation negative regulation of alpha-beta T cell differentiation negative regulation of lymphocyte activation leukocyte cell-cell adhesion leukocyte activation cell adhesion regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell-cell adhesion alpha-beta T cell activation involved in immune response CD4-positive, alpha-beta T cell activation lymphocyte activation involved in immune response regulation of lymphocyte differentiation regulation of T-helper 17 type immune response regulation of T cell activation T cell differentiation involved in immune response adaptive immune response negative regulation of T-helper cell differentiation negative regulation of cell activation negative regulation of immune system process regulation of hemopoiesis T-helper 17 type immune response cellular response to virus heart process system process regulation of heart contraction regulation of system process cardiac muscle contraction striated muscle contraction negative regulation of muscle contraction circulatory system process negative regulation of cardiac muscle contraction blood circulation negative regulation of blood circulation regulation of cardiac muscle contraction muscle contraction muscle system process regulation of muscle system process negative regulation of heart contraction regulation of blood circulation regulation of striated muscle contraction regulation of muscle contraction heart contraction negative regulation of striated muscle contraction regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	intracellular anatomical structure cytoplasm cellular anatomical entity rough endoplasmic reticulum membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus intracellular anatomical structure cytoplasm cellular anatomical entity rough endoplasmic reticulum membrane-bounded organelle intracellular organelle organelle endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system cytoskeleton intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-containing complex cytoplasmic ribonucleoprotein granule supramolecular complex ribonucleoprotein granule P-body organelle subcompartment membrane endoplasmic reticulum subcompartment bounding membrane of organelle rough endoplasmic reticulum membrane nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR021869	Ribonuclease Zc3h12a-like, NYN domain	Domain
A, B	IPR040546	Rege-1, UBA-like domain	Domain
A, B	IPR040757	Endoribonuclease Regnase 1/ZC3H12, C-terminal domain	Domain
A, B	IPR051101	ZC3H12/N4BP1 Ribonuclease and Regulator	Family

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.