Annotations: 9ZD1

Cryo-EM structure of ATR-ATRIP-TOPBP1 AAD

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08064	UME (NUC010) domain (UME)	UME (NUC010) domain	This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [1].	Domain
A, B	PF02260	FATC domain (FATC)	FATC domain	-	Family
A, B	PF23593	Serine/threonine-protein kinase ATR-like, HEAT repeats (HEAT_ATR)	Serine/threonine-protein kinase ATR-like, HEAT repeats	-	Repeat
A, B	PF25030	Serine/threonine-protein kinase ATR, M-HEAT region (M-HEAT_ATR)	Serine/threonine-protein kinase ATR, M-HEAT region	-	Repeat
A, B	PF00454	Phosphatidylinositol 3- and 4-kinase (PI3_PI4_kinase)	Phosphatidylinositol 3- and 4-kinase	-	Family
A, B	PF02259	FAT domain (FAT)	FAT domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth I], F [auth J]	DNA topoisomerase 2-binding protein 1	chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity DNA binding binding nucleic acid binding enzyme regulator activity protein serine/threonine kinase activator activity kinase activator activity enzyme activator activity molecular function activator activity molecular function regulator activity protein kinase activator activity protein kinase regulator activity kinase regulator activity identical protein binding protein binding phosphorylation-dependent protein binding modification-dependent protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process regulation of cell cycle phase transition signaling G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction mitotic cell cycle negative regulation of mitotic cell cycle cell communication mitotic G2/M transition checkpoint regulation of mitotic cell cycle mitotic DNA integrity checkpoint signaling negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle DNA replication checkpoint signaling regulation of cell cycle cell cycle process cell cycle G2/M phase transition regulation of biological process mitotic DNA replication checkpoint signaling negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process biological regulation DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process double-strand break repair via classical nonhomologous end joining double-strand break repair double-strand break repair via nonhomologous end joining DNA repair cellular component organization organelle organization chromosome organization cellular component organization or biogenesis localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to site of double-strand break intracellular protein localization homologous recombination DNA recombination response to ionizing radiation response to radiation response to abiotic stimulus DNA damage checkpoint signaling mitotic G2 DNA damage checkpoint signaling mitotic DNA damage checkpoint signaling signal transduction in response to DNA damage recombinational repair double-strand break repair via homologous recombination double-strand break repair via alternative nonhomologous end joining broken chromosome clustering	intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen intracellular organelle cellular anatomical structure intracellular anatomical structure cytoskeleton spindle organelle membraneless organelle intracellular membraneless organelle spindle pole microtubule cytoskeleton membrane-bounded organelle condensed nuclear chromosome nucleus membrane-enclosed lumen nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen organelle lumen condensed chromosome nuclear lumen centrosome microtubule organizing center nucleoplasm protein-containing complex BRCA1-B complex nuclear protein-containing complex male germ cell nucleus germ cell nucleus site of double-strand break site of DNA damage nuclear body PML body
C, D	ATR-interacting protein	polyubiquitin modification-dependent protein binding protein binding binding modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding	nucleobase-containing compound metabolic process primary metabolic process metabolic process cellular process cellular response to stimulus regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process cellular response to stress response to stress regulation of response to stress regulation of nucleobase-containing compound metabolic process nucleobase-containing compound metabolic process primary metabolic process metabolic process cellular process cellular response to stimulus regulation of cellular process regulation of double-strand break repair response to stimulus regulation of cellular response to stress regulation of primary metabolic process cellular response to stress response to stress regulation of response to stress regulation of nucleobase-containing compound metabolic process DNA repair double-strand break repair regulation of biological process biological regulation DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of DNA repair DNA damage response regulation of response to stimulus macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process DNA damage checkpoint signaling regulation of cell cycle phase transition signaling negative regulation of biological process negative regulation of cell cycle cell cycle phase transition intracellular signal transduction cell communication negative regulation of cellular process negative regulation of cell cycle phase transition signal transduction cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of cell cycle process cell cycle checkpoint signaling signal transduction in response to DNA damage	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen
A, B	Serine/threonine-protein kinase ATR	protein-containing complex binding binding MutSalpha complex binding mismatch repair complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding protein-containing complex binding binding MutSalpha complex binding mismatch repair complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups MutLalpha complex binding protein serine/threonine kinase activity histone H2AXS139 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity protein serine kinase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process response to chemical response to xenobiotic stimulus DNA-templated DNA replication DNA-templated DNA replication maintenance of fidelity primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process macromolecule metabolic process replication fork processing ribonucleoprotein complex biogenesis regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization telomerase catalytic core complex assembly positive regulation of biological process protein-RNA complex assembly cellular component biogenesis cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly protein-RNA complex organization protein-containing complex assembly cellular component organization or biogenesis positive regulation of cellular process positive regulation of telomerase catalytic core complex assembly regulation of biological process regulation of telomerase catalytic core complex assembly telomerase holoenzyme complex assembly protein-containing complex organization positive regulation of cellular component biogenesis biological regulation regulation of cellular component biogenesis replicative senescence cell cycle cell cycle process interstrand cross-link repair DNA repair membrane organization cellular component disassembly nuclear membrane disassembly membrane disassembly nuclear membrane organization nucleus organization organelle organization nuclear envelope organization endomembrane system organization positive regulation of cell communication positive regulation of signal transduction signaling regulation of cellular response to stress regulation of signal transduction DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of response to stress regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction regulation of DNA damage response, signal transduction by p53 class mediator regulation of signaling positive regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of intracellular signal transduction signal transduction by p53 class mediator regulation of response to stimulus regulation of cell communication signal transduction in response to DNA damage positive regulation of signaling positive regulation of organelle organization telomere organization regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process RNA-templated DNA biosynthetic process regulation of primary metabolic process telomere maintenance via telomere lengthening positive regulation of metabolic process positive regulation of telomere maintenance via telomere lengthening positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of telomere maintenance regulation of chromosome organization regulation of telomere maintenance via telomere lengthening regulation of organelle organization positive regulation of chromosome organization telomere maintenance biosynthetic process positive regulation of DNA metabolic process positive regulation of telomere maintenance via telomerase regulation of macromolecule biosynthetic process DNA biosynthetic process regulation of metabolic process regulation of DNA metabolic process regulation of telomere maintenance nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of biosynthetic process telomere maintenance via telomerase chromosome organization positive regulation of DNA biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process regulation of telomere maintenance via telomerase localization protein localization to chromosome protein localization to organelle macromolecule localization protein localization to chromosome, telomeric region intracellular protein localization regulation of cell cycle phase transition G2/M transition of mitotic cell cycle negative regulation of biological process negative regulation of cell cycle cell cycle phase transition mitotic cell cycle negative regulation of mitotic cell cycle mitotic G2/M transition checkpoint regulation of mitotic cell cycle negative regulation of cellular process negative regulation of cell cycle phase transition regulation of cell cycle cell cycle G2/M phase transition negative regulation of mitotic cell cycle phase transition regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process regulation of cell cycle G2/M phase transition negative regulation of cell cycle process cell cycle checkpoint signaling regulation of mitotic cell cycle phase transition mitotic cell cycle checkpoint signaling mitotic cell cycle process negative regulation of cell cycle G2/M phase transition negative regulation of G2/M transition of mitotic cell cycle mitotic cell cycle phase transition DNA damage checkpoint signaling DNA integrity checkpoint signaling response to arsenic-containing substance negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA replication negative regulation of metabolic process negative regulation of DNA metabolic process regulation of DNA replication cellular response to heat regulation of cellular response to heat response to heat response to temperature stimulus response to abiotic stimulus cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus response to ionizing radiation cellular response to gamma radiation response to radiation cellular response to abiotic stimulus response to gamma radiation regulation of double-strand break repair double-strand break repair regulation of DNA repair establishment of protein-containing complex localization to telomere establishment of localization response to mechanical stimulus response to external stimulus response to light stimulus response to UV cellular response to light stimulus cellular response to UV establishment of RNA localization to telomere establishment of RNA localization RNA localization	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex nuclear protein-containing complex ATR-ATRIP complex membraneless organelle membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex nuclear protein-containing complex ATR-ATRIP complex membraneless organelle intracellular membraneless organelle chromosome membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen site of DNA damage nuclear body PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth I], F [auth J]	IPR001357	BRCT domain	Domain
E [auth I], F [auth J]	IPR036420	BRCT domain superfamily	Homologous Superfamily
E [auth I], F [auth J]	IPR057595	TopBP1/SLF1, BRCT domain	Domain
E [auth I], F [auth J]	IPR035960	Secretoglobin superfamily	Homologous Superfamily
E [auth I], F [auth J]	IPR049936	TopBP1, eighth BRCT domain	Domain
E [auth I], F [auth J]	IPR044737	TopBP1, first BRCT domain	Domain
E [auth I], F [auth J]	IPR049542	TopBP1-like, BRCT0 domain	Domain
E [auth I], F [auth J]	IPR059215	DNA topoisomerase 2-binding protein 1-like, second BRCT domain	Domain
C, D	IPR060331	ATR-interacting protein, N-terminal	Domain
C, D	IPR033349	ATR-interacting protein	Family
C, D	IPR060332	ATR-interacting protein, C-terminal domain	Domain
A, B	IPR056802	Serine/threonine-protein kinase ATR-like, M-HEAT region	Domain
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR056803	Serine/threonine-protein kinase ATR-like, N-HEAT region	Domain
A, B	IPR012993	UME domain	Domain
A, B	IPR003151	PIK-related kinase, FAT	Domain
A, B	IPR057564	Serine/threonine-protein kinase ATR-like, HEAT repeats	Domain
A, B	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
A, B	IPR003152	FATC domain	Domain
A, B	IPR021133	HEAT, type 2	Repeat
A, B	IPR011989	Armadillo-like helical	Homologous Superfamily
A, B	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A, B	IPR050517	DNA Damage Response and Repair Kinase	Family
A, B	IPR018936	Phosphatidylinositol 3-/4-kinase, conserved site	Conserved Site
A, B	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B	IPR014009	PIK-related kinase, FAT domain	Domain

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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.

9ZD1 | pdb_00009zd1

Cryo-EM structure of ATR-ATRIP-TOPBP1 AAD

External Resource: Annotation

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage