|Entry||Database: EMDB / ID: 3669|
|Title||Closed dimer (C1) of human ATM (Ataxia telangiectasia mutated)|
|Map data||Closed dimer (C1) of human ATM (Ataxia telangiectasia mutated)|
|Sample||Dimeric human ATM (Ataxia telangiectasia mutated) kinase:|
Serine-protein kinase ATM
|Function / homology||Nonhomologous End-Joining (NHEJ) / Telomere-length maintenance and DNA damage repair / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3- and 4-kinases signature 1. / Processing of DNA double-strand break ends / FATC domain / TP53 Regulates Transcription of DNA Repair Genes / FAT domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily ...Nonhomologous End-Joining (NHEJ) / Telomere-length maintenance and DNA damage repair / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3- and 4-kinases signature 1. / Processing of DNA double-strand break ends / FATC domain / TP53 Regulates Transcription of DNA Repair Genes / FAT domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphatidylinositol 3/4-kinase, conserved site / FAT domain profile. / Armadillo-type fold / Serine/threonine-protein kinase ATM / PIK-related kinase / Protein kinase-like domain superfamily / FATC domain / PIK-related kinase, FAT / Phosphatidylinositol 3-/4-kinase, catalytic domain / Presynaptic phase of homologous DNA pairing and strand exchange / Phosphatidylinositol 3- and 4-kinases family profile. / Telomere-length maintenance and DNA damage repair / FATC domain profile. / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Resolution of D-loop Structures through Holliday Junction Intermediates / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Sensing of DNA Double Strand Breaks / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / HDR through Single Strand Annealing (SSA) / Meiotic recombination / HDR through Homologous Recombination (HRR) / Stabilization of p53 / Regulation of HSF1-mediated heat shock response / TP53 Regulates Transcription of Caspase Activators and Caspases / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Homologous DNA Pairing and Strand Exchange / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / positive regulation of DNA catabolic process / signal transduction involved in mitotic G2 DNA damage checkpoint / regulation of microglial cell activation / regulation of cellular response to gamma radiation / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / cellular response to nitrosative stress / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / pre-B cell allelic exclusion / meiotic telomere clustering / negative regulation of TORC1 signaling / cellular response to X-ray / immunoglobulin production / V(D)J recombination / lipoprotein catabolic process / female meiotic nuclear division / histone mRNA catabolic process / male meiotic nuclear division / oocyte development / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / positive regulation of histone phosphorylation / DNA repair complex / reciprocal meiotic recombination / DNA double-strand break processing / somitogenesis / response to ionizing radiation / mitotic spindle assembly checkpoint / DNA damage induced protein phosphorylation / negative regulation of B cell proliferation / determination of adult lifespan / histone phosphorylation / replicative senescence / regulation of autophagy / ovarian follicle development / post-embryonic development / telomere maintenance / positive regulation of telomere maintenance via telomerase / 1-phosphatidylinositol-3-kinase activity / double-strand break repair via nonhomologous end joining / thymus development / double-strand break repair via homologous recombination / multicellular organism growth / cellular response to gamma radiation / brain development / regulation of cellular response to heat / spindle / positive regulation of neuron apoptotic process / neuron apoptotic process / cell cycle arrest / intrinsic apoptotic signaling pathway in response to DNA damage / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / protein-containing complex binding / protein N-terminus binding|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 5.7 Å resolution|
|Authors||Baretic D / Pollard HK|
|Citation||Journal: Sci Adv / Year: 2017|
Title: Structures of closed and open conformations of dimeric human ATM.
Authors: Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams
|Validation Report||PDB-ID: 5np0|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 13, 2017 / Header (metadata) release: Apr 26, 2017 / Map release: May 17, 2017 / Last update: Feb 7, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3669.map.gz (map file in CCP4 format, 108001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.43 Å|
CCP4 map header:
-Entire Dimeric human ATM (Ataxia telangiectasia mutated) kinase
|Entire||Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase|
Details: homodimer / Number of components: 2
|Mass||Experimental: 705 kDa|
-Component #1: cellular-component, Dimeric human ATM (Ataxia telangiectasia muta...
|Cellular-component||Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase|
Details: homodimer / Recombinant expression: No
|Mass||Experimental: 705 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human) / Vector: pDEST12.2-OriP / Cell of expression system: HEK293|
-Component #2: protein, Serine-protein kinase ATM
|Protein||Name: Serine-protein kinase ATM / Recombinant expression: No|
|Mass||Theoretical: 352.393969 kDa|
|Source (engineered)||Expression System: Homo sapiens (human) / Vector: pDEST12.2-OriP / Cell of expression system: HEK293F|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.6 mg/ml / pH: 8|
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: 3 uL of sample/grid blotted for 12 s|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.1 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 97902 X (nominal), 35714 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4000 nm / Energy filter: GIF / Energy window: 0-20 eV|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.15 - K)|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Image acquisition||Number of digital images: 2720|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 25315|
|3D reconstruction||Software: RELION / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF|
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