5YWS | pdb_00005yws

Crystal structure of TREX1 in complex with a Y structured DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	Ribonuclease H-like	8034562	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8034562	3000143	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	DEAD	e5ywsA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (v294.1)
B	Yippee-Mis18	e5ywsB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Yippee-Mis18	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	A STEM LOOP DNA WITH Y-STRUCTURAL TERMINAL	-	-	-
A, B	Three-prime repair exonuclease 1	protein-containing complex binding binding MutSalpha complex binding mismatch repair complex binding protein binding WW domain binding protein domain specific binding DNA exonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity protein-containing complex binding binding MutSalpha complex binding mismatch repair complex binding protein binding WW domain binding protein domain specific binding DNA exonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity exonuclease activity DNA nuclease activity adenyl deoxyribonucleotide binding deoxyribonucleotide binding nucleotide binding purine deoxyribonucleotide binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding small molecule binding double-stranded DNA 3'-5' DNA exonuclease activity 3'-5' exonuclease activity double-stranded DNA exodeoxyribonuclease activity DNA exonuclease activity, producing 5'-phosphomonoesters 3'-5'-DNA exonuclease activity DNA binding nucleic acid binding identical protein binding MutLalpha complex binding cation binding magnesium ion binding ion binding metal ion binding double-stranded DNA binding protein homodimerization activity protein dimerization activity DNA binding, bending single-stranded DNA binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process macromolecule metabolic process regulation of protein stability biological regulation regulation of biological quality protein stabilization immune response immune system process adaptive immune response immune response in brain or nervous system organ or tissue specific immune response regulation of cellular process regulation of type I interferon-mediated signaling pathway negative regulation of biological process response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction regulation of biological process response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway regulation of response to stress negative regulation of cellular process innate immune response response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response regulation of protein complex stability regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process ribonucleotide catabolic process pyridine nucleotide catabolic process aerobic respiration oxoacid metabolic process carbohydrate catabolic process organophosphate catabolic process carbohydrate derivative metabolic process regulation of generation of precursor metabolites and energy nucleoside phosphate catabolic process organic acid metabolic process regulation of primary metabolic process regulation of ATP metabolic process regulation of purine nucleotide catabolic process regulation of small molecule metabolic process glycolytic process regulation of nucleotide metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process regulation of nucleobase-containing compound metabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process regulation of carbohydrate catabolic process pyruvate metabolic process purine nucleoside diphosphate metabolic process purine-containing compound catabolic process nucleotide metabolic process regulation of purine nucleotide metabolic process nucleoside diphosphate metabolic process purine nucleoside diphosphate catabolic process nucleoside diphosphate catabolic process regulation of nucleotide catabolic process regulation of phosphorus metabolic process nucleoside triphosphate metabolic process monocarboxylic acid metabolic process purine ribonucleotide metabolic process pyridine-containing compound catabolic process ribose phosphate metabolic process cellular respiration ATP metabolic process energy derivation by oxidation of organic compounds purine nucleotide metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine ribonucleoside triphosphate metabolic process ribonucleoside diphosphate metabolic process ribonucleoside diphosphate catabolic process regulation of carbohydrate metabolic process nucleotide catabolic process purine nucleoside triphosphate metabolic process purine nucleotide catabolic process carbohydrate metabolic process carbohydrate derivative catabolic process ADP catabolic process carboxylic acid metabolic process regulation of catabolic process generation of precursor metabolites and energy regulation of glycolytic process purine-containing compound metabolic process ADP metabolic process organophosphate metabolic process purine ribonucleoside diphosphate metabolic process purine ribonucleoside diphosphate catabolic process regulation of cell cycle phase transition DNA damage checkpoint signaling negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling mitotic DNA damage checkpoint signaling negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic G1 DNA damage checkpoint signaling mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle signal transduction in response to DNA damage G1/S transition of mitotic cell cycle mitotic cell cycle phase transition cellular response to interferon-beta response to interferon-beta response to oxidative stress cellular response to chemical stimulus cellular response to oxidative stress cellular response to chemical stress developmental process heart development multicellular organismal process heart morphogenesis animal organ development circulatory system development multicellular organism development anatomical structure morphogenesis anatomical structure development animal organ morphogenesis system development carbohydrate derivative biosynthetic process glycoprotein biosynthetic process glycoprotein metabolic process protein metabolic process macrophage activation involved in immune response cell activation cell activation involved in immune response myeloid cell activation involved in immune response myeloid leukocyte activation leukocyte activation immune effector process macrophage activation leukocyte activation involved in immune response transposition retrotransposition inflammatory response inflammatory response to antigenic stimulus regulation of leukocyte activation regulation of cell activation regulation of T cell activation lymphocyte activation T cell activation regulation of multicellular organismal process regulation of lymphocyte activation response to light stimulus response to radiation response to abiotic stimulus response to UV vasculature development blood vessel development defense response to virus response to virus DNA synthesis involved in DNA repair cellular response to environmental stimulus nucleic acid biosynthetic process cellular response to light stimulus DNA repair cellular response to radiation nucleobase-containing compound biosynthetic process UV-damage excision repair cellular response to abiotic stimulus cellular response to UV DNA synthesis involved in UV-damage excision repair DNA biosynthetic process kidney development renal system development positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway cGAS/STING signaling pathway immune response-activating signaling pathway positive regulation of immune response positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cGAS/STING signaling pathway regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response activation of immune response cytoplasmic pattern recognition receptor signaling pathway intracellular receptor signaling pathway negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction positive regulation of biological process regulation of cytoplasmic pattern recognition receptor signaling pathway positive regulation of response to stimulus positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction positive regulation of innate immune response localization import into cell transport phagocytosis apoptotic cell clearance endocytosis establishment of localization vesicle-mediated transport DNA replication establishment of protein localization fatty acid metabolic process ketone metabolic process regulation of lipid metabolic process regulation of ketone metabolic process regulation of fatty acid metabolic process lipid metabolic process type I interferon production cytokine production regulation of cytokine production regulation of type I interferon production DNA modification macromolecule modification cellular response to ionizing radiation response to ionizing radiation cellular response to gamma radiation response to gamma radiation regulation of cellular component organization vacuole organization lytic vacuole organization regulation of vacuole organization regulation of organelle organization cellular component organization lysosome organization organelle organization regulation of lysosome organization cellular component organization or biogenesis heart process system process circulatory system process regulation of tumor necrosis factor production tumor necrosis factor superfamily cytokine production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production cellular developmental process hemopoiesis cell differentiation lymphoid progenitor cell differentiation cell development hematopoietic progenitor cell differentiation lipid biosynthetic process regulation of lipid biosynthetic process determination of adult lifespan response to oxygen-containing compound cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species regulation of inflammatory response production of molecular mediator of immune response regulation of immune effector process immunoglobulin production regulation of immunoglobulin production regulation of production of molecular mediator of immune response adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity T cell mediated immunity T cell antigen processing and presentation antigen processing and presentation leukocyte mediated immunity cardiac muscle tissue development tissue development atrial cardiac muscle tissue development striated muscle tissue development muscle tissue development cellular response to nitrogen compound cellular response to hydroxyurea response to hydroxyurea response to nitrogen compound regulation of cellular respiration immunoglobulin mediated immune response B cell mediated immunity immune complex formation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen nuclear replication fork intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle membraneless organelle replication fork nuclear lumen protein-containing complex catalytic complex organelle subcompartment oligosaccharyltransferase complex membrane membrane protein complex transferase complex endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR040393	Three-prime repair exonuclease 1/2	Family
A, B	IPR013520	Ribonuclease H-like domain	Domain
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily

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.