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- PDB-5np1: Open protomer of human ATM (Ataxia telangiectasia mutated) -

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Database: PDB / ID: 5np1
TitleOpen protomer of human ATM (Ataxia telangiectasia mutated)
ComponentsSerine-protein kinase ATM
KeywordsTRANSFERASE / FAT / MRN / DNA-repair / HEAT-repeats / Transferase
Function / homologyNonhomologous 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
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 5.7 Å resolution
AuthorsBaretic, 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.
CitationJournal: 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
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2017 / Release: May 17, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 17, 2017Structure modelrepositoryInitial release
1.1May 31, 2017Structure modelDatabase references
1.2Jul 26, 2017Structure modelData collection / Experimental preparationem_imaging_optics / em_sample_support / em_software_em_imaging_optics.energyfilter_name / _em_software.details / _em_software.name
1.3Aug 30, 2017Structure modelAuthor supporting evidence / Data collectionem_imaging_optics / pdbx_audit_support_em_imaging_optics.energyfilter_name / _pdbx_audit_support.funding_organization
1.4Jan 31, 2018Structure modelData processing / Experimental preparationem_sample_support / em_software_em_sample_support.grid_type / _em_software.details / _em_software.name
1.5Feb 7, 2018Structure modelData collectionem_imaging_optics_em_imaging_optics.energyfilter_lower

Structure visualization

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Deposited unit
A: Serine-protein kinase ATM

Theoretical massNumber of molelcules
Total (without water)352,3941

  • idetical with deposited unit
  • defined by author
  • Evidence: light scattering, SEC-MALS indicates monodisperse sample of 0.7 MDa.
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide Serine-protein kinase ATM / Ataxia telangiectasia mutated / A-T mutated

Mass: 352393.969 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293 / Gene: ATM / Plasmid name: pDEST12.2-OriP / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
References: UniProt: Q13315, non-specific serine/threonine protein kinase

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Molecular weightValue: 0.705 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: HEK293 / Organism: Homo sapiens (human) / Plasmid: pDEST12.2-OriP
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
125 mMHEPES pH 7.51
225 mMTris pH 8.81
3150 mMsodium chlorideNaCl1
40.01 %Tween 201
52 mMTCEP1
SpecimenConc.: 0.6 mg/ml
Details: The sample was purified by anti-FLAG affinity chromatography followed by overnight dialysis and a final gel-filtration.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen support
IDSpecimen IDGrid materialGrid mesh sizeGrid type
11GOLD300Quantifoil R1.2/1.3
21GOLD300Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins
Details: 3 uL sample/grid blotted for 12 s before plunge-freezing

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80.15 kelvins
Image recordingAverage 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 opticsEnergyfilter name: GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 20 / Used frames/image: 1-20


SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
1Gautomatchv0.5particle selection
3UCSFImage4image acquisition
5Gctfv0.5CTF correction
8Coot0.8.1model fitting
10PHENIX1.10.1_2155model refinementphenix_real_space
11RELION1.4initial Euler assignment
12RELION1.4final Euler assignment
14RELION1.43D reconstruction
Particle selectionNumber of particles selected: 371671
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 60556 / Number of class averages: 2 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01312184
ELECTRON MICROSCOPYf_angle_d1.38916923
ELECTRON MICROSCOPYf_dihedral_angle_d7.8577153
ELECTRON MICROSCOPYf_chiral_restr0.0532367
ELECTRON MICROSCOPYf_plane_restr0.0092419

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