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- PDB-5np0: Closed dimer of human ATM (Ataxia telangiectasia mutated) -

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Database: PDB / ID: 5np0
TitleClosed dimer of human ATM (Ataxia telangiectasia mutated)
DescriptorSerine-protein kinase ATM (E.C.
KeywordsSIGNALING PROTEIN / PIKK / kinase / DNA-repair / HEAT-repeats
Specimen sourceHomo sapiens / human
MethodElectron microscopy (5.7 Å resolution / Particle / Single particle)
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.
CitationSci Adv, 2017, 3, e1700933-e1700933

Sci Adv, 2017, 3, e1700933-e1700933 Yorodumi Papers
Structures of closed and open conformations of dimeric human ATM.
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

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Deposited unit
A: Serine-protein kinase ATM
B: Serine-protein kinase ATM

Theoretical massNumber of molelcules
Total (without water)704,7882

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1


#1: Polypeptide(L)Serine-protein kinase ATM / Ataxia telangiectasia mutated / A-T mutated

Mass: 352393.969 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: Q13315, EC:

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Type: ORGANELLE OR CELLULAR COMPONENT / Details: homodimer / Entity ID: 1 / Source: RECOMBINANT
Molecular weightValue: 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 solutionpH: 8
Buffer component
IDConc.UnitsNameFormulaBuffer ID
125mMHEPES pH 7.51
225mMTris pH 8.81
3150mMsodium chlorideNaCl1
40.01%Tween 201
SpecimenConc.: 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
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 of sample/grid blotted for 12 s

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 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 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
Image scansMovie frames/image: 20 / Used frames/image: 1-20


SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryImage processing IDImaging IDFitting IDDetails
10PHENIX1.10.1_2155MODEL REFINEMENT1Phenix_real_space
Particle selectionNumber of particles selected: 371671
SymmetryPoint symmetry: C1
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25315 / Number of class averages: 1 / Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-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
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.02424984
ELECTRON MICROSCOPYf_angle_d1.47934710
ELECTRON MICROSCOPYf_dihedral_angle_d7.28614666
ELECTRON MICROSCOPYf_chiral_restr0.0494850
ELECTRON MICROSCOPYf_plane_restr0.0114966

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