|Entry||Database: PDB / ID: 5np0|
|Title||Closed dimer of human ATM (Ataxia telangiectasia mutated)|
|Components||Serine-protein kinase ATM|
|Keywords||SIGNALING PROTEIN / PIKK / kinase / DNA-repair / HEAT-repeats|
|Function/homology||Serine/threonine-protein kinase ATM / regulation of cellular response to gamma radiation / regulation of microglial cell activation / positive regulation of DNA catabolic process / signal transduction involved in mitotic G2 DNA damage checkpoint / positive regulation of telomerase catalytic core complex assembly / establishment of RNA localization to telomere / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / positive regulation of telomere maintenance via telomere lengthening ...Serine/threonine-protein kinase ATM / regulation of cellular response to gamma radiation / regulation of microglial cell activation / positive regulation of DNA catabolic process / signal transduction involved in mitotic G2 DNA damage checkpoint / positive regulation of telomerase catalytic core complex assembly / establishment of RNA localization to telomere / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / cellular response to nitrosative stress / pre-B cell allelic exclusion / Sensing of DNA Double Strand Breaks / 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 / meiotic telomere clustering / negative regulation of TORC1 signaling / cellular response to X-ray / immunoglobulin production / V(D)J recombination / histone mRNA catabolic process / lipoprotein catabolic process / female meiotic nuclear division / male meiotic nuclear division / PIK-related kinase, FAT / oocyte development / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / FAT domain profile. / FATC domain profile. / PIK-related kinase / FATC domain / positive regulation of histone phosphorylation / reciprocal meiotic recombination / DNA repair complex / FAT domain / FATC domain / Homologous DNA Pairing and Strand Exchange / strand displacement / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / DNA double-strand break processing / Resolution of D-loop Structures through Holliday Junction Intermediates / somitogenesis / response to ionizing radiation / mitotic spindle assembly checkpoint / HDR through Single Strand Annealing (SSA) / DNA synthesis involved in DNA repair / DNA damage induced protein phosphorylation / TP53 Regulates Transcription of Caspase Activators and Caspases / Phosphatidylinositol 3- and 4-kinases signature 1. / negative regulation of B cell proliferation / Presynaptic phase of homologous DNA pairing and strand exchange / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3- and 4-kinases family profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Phosphatidylinositol 3-/4-kinase, catalytic domain / determination of adult lifespan / replicative senescence / Regulation of HSF1-mediated heat shock response / histone phosphorylation / regulation of autophagy / ovarian follicle development / Nonhomologous End-Joining (NHEJ) / post-embryonic development / positive regulation of telomere maintenance via telomerase / telomere maintenance / TP53 Regulates Transcription of DNA Repair Genes / Phosphatidylinositol 3- and 4-kinase / 1-phosphatidylinositol-3-kinase activity / double-strand break repair via nonhomologous end joining / Autodegradation of the E3 ubiquitin ligase COP1 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / thymus development / Stabilization of p53 / HDR through Homologous Recombination (HRR) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / cellular response to gamma radiation / Regulation of TP53 Activity through Methylation / brain development / regulation of cellular response to heat / Meiotic recombination / spindle / positive regulation of neuron apoptotic process / neuron apoptotic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cell cycle arrest / intrinsic apoptotic signaling pathway in response to DNA damage / Regulation of TP53 Degradation / Processing of DNA double-strand break ends / protein N-terminus binding / heart development / Armadillo-type fold / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|
Function and homology information
|Specimen source||Homo sapiens / human /|
|Method||Electron microscopy (5.7 Å resolution / Particle / Single particle) / Transmission electron microscopy|
|Authors||Baretic, D. / Pollard, H.K. / Fisher, D.I. / Johnson, C.M. / Santhanam, B. / Truman, C.M. / Kouba, T. / Fersht, A.R. / Phillips, C. / Williams, R.L.|
|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
Abstract: ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, ...ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
SummaryFull reportAbout validation report
|Date||Deposition: Apr 13, 2017 / Release: May 17, 2017|
Downloads & links
A: Serine-protein kinase ATM
B: Serine-protein kinase ATM
Mass: 352393.969 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / / Cell line: HEK293F / Gene: ATM / Plasmid name: pDEST12.2-OriP / Cell line (production host): HEK293F / Production host: Homo sapiens
References: UniProt:Q13315, EC:126.96.36.199 (non-specific serine/threonine protein kinase)
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase|
Type: ORGANELLE OR CELLULAR COMPONENT / Details: homodimer / Entity ID: 1 / Source: RECOMBINANT
|Molecular weight||Value: 0.705 deg. / Units: MEGADALTONS / Experimental value: YES|
|Source (natural)||Organism: Homo sapiens|
|Source (recombinant)||Cell: HEK293 / Organism: Homo sapiens / Plasmid: pDEST12.2-OriP|
|Buffer solution||pH: 8|
|Specimen||Conc.: 0.6 mg/ml|
Details: N-terminally FLAG-tagged ATM kinase was purified by affinity chromatography (anti-FLAG), overnight dialysis and gel-filtration. The sample was flash-frozen in liquid nitrogen until used for cryo-EM.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Vitrification||Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: 3 uL of sample/grid blotted for 12 s|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 97902 / Calibrated magnification: 35714 / Nominal defocus max: 4000 nm / Nominal defocus min: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80.15 kelvins|
|Image recording||Average exposure time: 0.8 sec. / Electron dose: 2.1 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 4 / Number of real images: 2720|
|EM imaging optics||Energyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV|
|Image scans||Movie frames/image: 20 / Used frames/image: 1-20|
|Software||Name: PHENIX / Version: 1.10.1_2155: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING ONLY|
|Particle selection||Number of particles selected: 371671|
|Symmetry||Point symmetry: C1|
|3D reconstruction||Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25315 / Number of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Ref space: REAL|
|Atomic model building||PDB-ID: 4JSP|
Details: building de novo the structure of ATM N-solenoid and modelling of the ATM FATKIN (using mTOR FATKIN PDB:4JSP)
|Refine LS restraints|
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