6K9L

4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase

External Resource: Annotation

Domain Annotation: ECOD Classification
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	PI3_PI4_kinase	e6k9lA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PI3_PI4_kinase	ECOD (1.6)
B	PI3_PI4_kinase	e6k9lB1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: PI3_PI4_kinase	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF11640	Telomere-length maintenance and DNA damage repair (TAN)	Telomere-length maintenance and DNA damage repair	ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of th ...	ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage [1]. It is classified as an EC:2.7.11.1.	Domain
A, B	PF02260	FATC domain (FATC)	FATC domain	-	Family
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
A, B	Serine-protein kinase ATM	protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity DNA-dependent protein kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity DNA-dependent protein kinase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding protein-containing complex binding phosphatidylinositol kinase activity lipid kinase activity 1-phosphatidylinositol-3-kinase activity identical protein binding protein binding histone H2AXS139 kinase activity histone modifying activity histone kinase activity histone H2AX kinase activity protein serine kinase activity	developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development establishment of organelle localization meiotic chromosome segregation cellular localization sexual reproduction reproductive process meiotic cell cycle process developmental process heart development multicellular organism development multicellular organismal process anatomical structure development animal organ development circulatory system development system development establishment of organelle localization meiotic chromosome segregation cellular localization sexual reproduction reproductive process meiotic cell cycle process cellular component organization localization telomere localization meiosis I chromosome localization organelle localization establishment of localization in cell meiotic nuclear division cell cycle cellular component organization or biogenesis chromosome segregation cell cycle process meiotic cell cycle organelle fission meiotic telomere clustering chromosome organization establishment of localization chromosome organization involved in meiotic cell cycle nuclear division organelle organization chromosome localization to nuclear envelope involved in homologous chromosome segregation meiosis I cell cycle process nuclear chromosome segregation cellular process homologous chromosome segregation establishment of chromosome localization homologous recombination nucleobase-containing compound metabolic process reciprocal homologous recombination DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process reciprocal meiotic recombination metabolic process macromolecule metabolic process catabolic process regulation of cellular component organization regulation of cellular process macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component assembly process utilizing autophagic mechanism regulation of biological process autophagosome assembly organelle assembly vacuole organization regulation of autophagosome assembly biological regulation regulation of vacuole organization regulation of cellular component biogenesis regulation of organelle organization regulation of organelle assembly ribonucleoprotein complex biogenesis positive regulation of cellular component organization telomerase catalytic core complex assembly positive regulation of biological process protein-RNA complex assembly regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly protein-RNA complex organization protein-containing complex assembly positive regulation of cellular process positive regulation of telomerase catalytic core complex assembly regulation of telomerase catalytic core complex assembly telomerase holoenzyme complex assembly protein-containing complex organization positive regulation of cellular component biogenesis replicative senescence cellular response to stimulus response to lipid response to stimulus response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid response to chemical cellular response to lipid response to X-ray cellular response to ionizing radiation cellular response to radiation cellular response to environmental stimulus cellular response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus cellular response to abiotic stimulus protein phosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process 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 positive regulation of nucleobase-containing compound metabolic process regulation of chromosome organization regulation of telomere maintenance via telomere lengthening 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 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 multicellular organism growth developmental growth growth negative regulation of telomere maintenance negative regulation of biological process negative regulation of chromosome organization negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of cellular component organization negative regulation of metabolic process negative regulation of organelle organization telomere capping negative regulation of telomere capping negative regulation of DNA metabolic process regulation of telomere capping somitogenesis epithelium development chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development tissue development regionalization anatomical structure morphogenesis embryo development ending in birth or egg hatching somite development anatomical structure formation involved in morphogenesis regulation of cell cycle phase transition spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction mitotic sister chromatid separation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling regulation of cell cycle process sister chromatid segregation regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle signaling spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle regulation of mitotic cell cycle mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition regulation of cell cycle negative regulation of chromosome separation mitotic nuclear division negative regulation of mitotic cell cycle phase transition negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling negative regulation of chromosome segregation chromosome separation negative regulation of nuclear division regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition cellular developmental process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development cell differentiation germ cell development oocyte differentiation autophagy of peroxisome pexophagy macromolecule catabolic process regulation of DNA catabolic process positive regulation of DNA catabolic process DNA catabolic process regulation of catabolic process nucleobase-containing compound catabolic process positive regulation of catabolic process nucleic acid catabolic process cell adhesion positive regulation of cell adhesion regulation of cell adhesion DNA damage checkpoint signaling G2/M transition of mitotic cell cycle mitotic G2 DNA damage checkpoint signaling mitotic G2/M transition checkpoint mitotic DNA integrity checkpoint signaling cellular response to stress response to stress mitotic DNA damage checkpoint signaling cell cycle G2/M phase transition regulation of G2/M transition of mitotic cell cycle DNA integrity checkpoint signaling regulation of cell cycle G2/M phase transition DNA damage response negative regulation of cell cycle G2/M phase transition signal transduction in response to DNA damage negative regulation of G2/M transition of mitotic cell cycle neuron apoptotic process apoptotic process cell death programmed cell death positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion regulation of signaling regulation of signal transduction signal transduction by p53 class mediator regulation of intracellular signal transduction regulation of response to stimulus regulation of signal transduction by p53 class mediator regulation of cell communication lipoprotein metabolic process protein catabolic process lipoprotein catabolic process establishment of RNA localization to telomere establishment of RNA localization macromolecule localization RNA localization head development central nervous system development brain development nervous system development double-strand break repair DNA double-strand break processing DNA repair negative regulation of lymphocyte proliferation 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 multicellular organismal process regulation of immune system 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 gene expression regulation of gene expression positive regulation of gene expression positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process male meiotic nuclear division male gamete generation cellular senescence RNA metabolic process RNA catabolic process histone mRNA catabolic process mRNA catabolic process nuclear-transcribed mRNA catabolic process histone mRNA metabolic process mRNA metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process protein autophosphorylation gonad development reproductive system development female gonad development sex differentiation female sex differentiation development of primary female sexual characteristics development of primary sexual characteristics reproductive structure development ovarian follicle development positive regulation of cell communication positive regulation of signal transduction regulation of cellular response to stress DNA damage response, signal transduction by p53 class mediator positive regulation of response to stimulus regulation of response to stress positive regulation of signal transduction by p53 class mediator regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of DNA damage response, signal transduction by p53 class mediator positive regulation of intracellular signal transduction positive regulation of signaling response to decreased oxygen levels response to hypoxia response to oxygen levels peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification immature B cell differentiation mononuclear cell differentiation pre-B cell allelic exclusion pre-B cell differentiation lymphocyte differentiation B cell differentiation hemopoiesis leukocyte differentiation positive regulation of DNA-templated transcription RNA biosynthetic process DNA-templated transcription regulation of RNA metabolic process 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 positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription cellular response to heat regulation of cellular response to heat response to heat response to temperature stimulus immune system development gland development hematopoietic or lymphoid organ development thymus development cellular response to gamma radiation response to gamma radiation regulation of macrophage activation regulation of defense response regulation of response to external stimulus myeloid leukocyte activation macrophage activation leukocyte activation involved in inflammatory response regulation of neuroinflammatory response defense response regulation of inflammatory response response to external stimulus microglial cell activation regulation of microglial cell activation inflammatory response glial cell activation neuroinflammatory response female meiotic nuclear division response to nitrosative stress cellular response to nitrosative stress cellular response to chemical stress establishment of protein-containing complex localization to telomere cellular macromolecule localization protein-containing complex localization determination of adult lifespan apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage intrinsic apoptotic signaling pathway cellular response to oxidative stress response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress recombinational repair double-strand break repair via homologous recombination cell cycle G1/S phase transition negative regulation of G1/S transition of mitotic cell cycle mitotic G1/S transition checkpoint signaling regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle regulation of cell cycle G1/S phase transition negative regulation of cell cycle G1/S phase transition mitotic G1 DNA damage checkpoint signaling DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of TORC1 signaling negative regulation of TOR signaling regulation of TORC1 signaling TOR signaling regulation of TOR signaling negative regulation of response to stimulus negative regulation of signal transduction TORC1 signaling peptidyl-serine autophosphorylation regulation of autophagy post-embryonic development double-strand break repair via nonhomologous end joining somatic cell DNA recombination V(D)J recombination somatic diversification of immune receptors via germline recombination within a single locus somatic diversification of immune receptors	protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol peroxisomal matrix membrane-bounded organelle peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex catalytic complex DNA repair complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol peroxisomal matrix membrane-bounded organelle peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle microbody lumen microbody nucleus intracellular membraneless organelle nucleolus membraneless organelle nuclear lumen cytoplasmic vesicle intracellular vesicle vesicle site of double-strand break site of DNA damage chromosome cytoskeleton spindle microtubule cytoskeleton centrosome microtubule organizing center nucleoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR016024	Armadillo-type fold	Homologous Superfamily
A, B	IPR038980	Serine/threonine-protein kinase ATM, plant	Family
A, B	IPR018936	Phosphatidylinositol 3/4-kinase, conserved site	Conserved Site
A, B	IPR021668	Telomere-length maintenance and DNA damage repair	Domain
A, B	IPR044107	ATM, catalytic domain	Domain
A, B	IPR036940	Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily	Homologous Superfamily
A, B	IPR014009	PIK-related kinase	Domain
A, B	IPR003151	PIK-related kinase, FAT	Domain
A, B	IPR003152	FATC domain	Domain
A, B	IPR000403	Phosphatidylinositol 3-/4-kinase, catalytic domain	Domain
A, B	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q13315	ataxia telangiectasia melanoma B-cell chronic lymphocytic leukemia urinary bladder cancer mature T-cell and NK-cell non-Hodgkin lymphoma dilated cardiomyopathy cancer mantle cell lymphoma adenoid cystic carcinoma neurodegenerative disease breast carcinoma cataract primary cutaneous T-cell non-Hodgkin lymphoma prostate cancer Fibrosis ataxia telangiectasia melanoma B-cell chronic lymphocytic leukemia urinary bladder cancer mature T-cell and NK-cell non-Hodgkin lymphoma dilated cardiomyopathy cancer mantle cell lymphoma adenoid cystic carcinoma neurodegenerative disease breast carcinoma cataract primary cutaneous T-cell non-Hodgkin lymphoma prostate cancer Fibrosis cutaneous melanoma medulloblastoma myocardial infarction salivary gland adenoid cystic carcinoma hepatocellular carcinoma squamous cell carcinoma breast cancer colorectal adenocarcinoma primary cutaneous T-cell lymphoma diabetes mellitus malignant pancreatic neoplasm prostate adenocarcinoma dilated cardiomyopathy 1A prostate carcinoma gastric cancer glioma myopathy schizophrenia hereditary ataxia stomach carcinoma in situ benign neoplasm of stomach large cell medulloblastoma osteosarcoma brain disease uterine corpus leiomyoma ovarian disease lymphatic system disease peripheral nervous system disease malignant ependymoma malignant mesothelioma Pick disease digestive system disease prostate disease gastric carcinoma multiple sclerosis astrocytic tumor renal cell carcinoma granulomatous slack skin disease atypical teratoid rhabdoid tumor Sjogren syndrome hereditary breast carcinoma T-cell prolymphocytic leukemia Nijmegen breakage syndrome bladder benign neoplasm urinary bladder carcinoma ovarian cancer breast adenocarcinoma lung adenocarcinoma ovarian neoplasm breast disease lymphoma peripheral neuropathy progressive supranuclear palsy gastric adenocarcinoma gastric neoplasm ataxia - telangiectasia variant autosomal recessive cerebellar ataxia hereditary diffuse gastric adenocarcinoma benign neoplasm ulcerative colitis oligodendroglioma bladder carcinoma in situ urinary bladder neoplasm leukemia ovarian carcinoma lung disease pancreatic neoplasm

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.