|Entry||Database: EMDB / ID: 3672|
|Title||Open protomer of human ATM (Ataxia telangiectasia mutated)|
|Map data||Open protomer of human ATM (Ataxia telangiectasia mutated)|
|Sample||Dimeric human ATM (Ataxia telangiectasia mutated) kinase:|
Serine-protein kinase ATM
|Function / homology||HDR through Homologous Recombination (HRR) / Serine/threonine-protein kinase ATM / Phosphatidylinositol 3- and 4-kinase / Processing of DNA double-strand break ends / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Telomere-length maintenance and DNA damage repair / Homologous DNA Pairing and Strand Exchange / Nonhomologous End-Joining (NHEJ) / Phosphatidylinositol 3/4-kinase, conserved site / Armadillo-type fold ...HDR through Homologous Recombination (HRR) / Serine/threonine-protein kinase ATM / Phosphatidylinositol 3- and 4-kinase / Processing of DNA double-strand break ends / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Telomere-length maintenance and DNA damage repair / Homologous DNA Pairing and Strand Exchange / Nonhomologous End-Joining (NHEJ) / Phosphatidylinositol 3/4-kinase, conserved site / Armadillo-type fold / PIK-related kinase / FATC domain / Protein kinase-like domain superfamily / FATC domain / PIK-related kinase, FAT / Resolution of D-loop Structures through Holliday Junction Intermediates / Phosphatidylinositol 3-/4-kinase, catalytic domain / 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 / FAT domain / Presynaptic phase of homologous DNA pairing and strand exchange / Telomere-length maintenance and DNA damage repair / Regulation of TP53 Degradation / HDR through Single Strand Annealing (SSA) / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of HSF1-mediated heat shock response / Meiotic recombination / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / FATC domain profile. / Regulation of TP53 Activity through Phosphorylation / FAT domain profile. / TP53 Regulates Transcription of Caspase Activators and Caspases / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TP53 Regulates Transcription of DNA Repair Genes / Phosphatidylinositol 3- and 4-kinases family profile. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3- and 4-kinases signature 1. / signal transduction involved in mitotic G2 DNA damage checkpoint / regulation of cellular response to gamma radiation / regulation of microglial cell activation / positive regulation of DNA catabolic process / positive regulation of telomerase catalytic core complex assembly / establishment of RNA localization to telomere / DNA-dependent protein kinase activity / cellular response to nitrosative stress / positive regulation of telomere maintenance via telomere lengthening / 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 / negative regulation of TORC1 signaling / cellular response to X-ray / histone mRNA catabolic process / regulation of telomere maintenance via telomerase / positive regulation of histone phosphorylation / peptidyl-serine autophosphorylation / reciprocal meiotic recombination / DNA repair complex / DNA double-strand break processing / response to ionizing radiation / DNA damage induced protein phosphorylation / mitotic spindle assembly checkpoint / negative regulation of B cell proliferation / positive regulation of cell adhesion / histone phosphorylation / replicative senescence / regulation of autophagy / positive regulation of telomere maintenance via telomerase / telomere maintenance / cellular response to retinoic acid / 1-phosphatidylinositol-3-kinase activity / cellular response to gamma radiation / regulation of cellular response to heat / double-strand break repair via nonhomologous end joining / cell cycle arrest / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of neuron apoptotic process / protein N-terminus binding / cytoplasmic vesicle / regulation of signal transduction by p53 class mediator / regulation of apoptotic process / response to hypoxia / DNA replication / protein-containing complex binding / protein dimerization activity / non-specific serine/threonine protein kinase / peptidyl-serine phosphorylation / protein autophosphorylation / positive regulation of cell migration / positive regulation of apoptotic process / DNA repair / cellular response to DNA damage stimulus / apoptotic process / nucleolus / positive regulation of gene expression|
Function and homology information
|Source||Homo sapiens (human)|
|Method||single particle reconstruction / cryo EM / 5.7 Å resolution|
|Authors||Baretic D / Pollard HK / Fisher DI / Johnson CM / Santhanam B / Truman CM / Kouba T / Fersht AR / Phillips C / Williams RL|
|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: 5np1|
SummaryFull reportAbout validation report
|Date||Deposition: Apr 13, 2017 / Header (metadata) release: Apr 26, 2017 / Map release: May 17, 2017 / Last update: Oct 24, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3672.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|
Number of components: 2
-Component #1: cellular-component, Dimeric human ATM (Ataxia telangiectasia muta...
|Cellular-component||Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase|
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 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 352.393969 kDa|
|Source||Species: Homo sapiens (human)|
|Source (engineered)||Expression System: Homo sapiens (human)|
|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 sample/grid blotted for 12 s before plunge-freezing.
-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: 97902.0 X (nominal), 35714.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500.0 - 4000.0 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 SUMMIT (4k x 4k)|
|Image acquisition||Number of digital images: 2720|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 60556|
|3D reconstruction||Software: RELION / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
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