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- EMDB-6399: Structure of the intact ATM/Tel1 kinase -

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Basic information

Entry
Database: EMDB / ID: 6399
TitleStructure of the intact ATM/Tel1 kinase
Map dataReconstruction of ATM/Tel1
SampleEndogenous ATM/Tel1 purified directly from the yeast cells:
ATM/Tel1
KeywordsATM/Tel1 / DSB / kinase activity
SourceSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / 8.7 Å resolution
AuthorsWang XJ / Chu HY / Lv MJ / Zhang ZH / Qiu SW / Liu HY / Shen XT / Wang WW / Cai G
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the intact ATM/Tel1 kinase.
Authors: Xuejuan Wang / Huanyu Chu / Mengjuan Lv / Zhihui Zhang / Shuwan Qiu / Haiyan Liu / Xuetong Shen / Weiwu Wang / Gang Cai
DateDeposition: Jul 28, 2015 / Header (metadata) release: Nov 18, 2015 / Map release: Jul 27, 2016 / Last update: Jul 27, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.067
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6399.map.gz (map file in CCP4 format, 65537 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.42 Å/pix.
= 363.52 Å
256 pix
1.42 Å/pix.
= 363.52 Å
256 pix
1.42 Å/pix.
= 363.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density
Contour Level:0.067 (by author), 0.067 (movie #1):
Minimum - Maximum-0.0982672 - 0.25424597
Average (Standard dev.)0.00141853 (0.01484582)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 363.52 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z363.520363.520363.520
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0980.2540.001

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Supplemental data

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Sample components

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Entire Endogenous ATM/Tel1 purified directly from the yeast cells

EntireName: Endogenous ATM/Tel1 purified directly from the yeast cells
Number of components: 1
Oligomeric State: An asymmetric homo-dimeric architecture with pseudo C2 symmetry
MassTheoretical: 700 kDa / Experimental: 700 kDa / Measured by: Sedimentation

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Component #1: protein, ATM/Tel1

ProteinName: ATM/Tel1 / Oligomeric Details: Dimer / Recombinant expression: No / Number of Copies: 2
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Schizosaccharomyces pombe (fission yeast) / Strain: CC5060

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining, cryo EM
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 50mmol/L Tris, 100mmol/L ammonium sulfate, 10%(v/v) glycerol, 1mmol/L EDTA, 10umol/L ZnSO4, 0.02% NP-40, 10mmol/b-ME
pH: 7.6
Support filma carbon-coated 400-mesh Cu EM specimen grid freshly glow discharged
StainingSample was applied to a carbon-coated 400-mesh Cu EM specimen grid freshly glow discharged and was then preserved by staining with 0.75%(w/w) uranyl formate solution.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 120 K / Humidity: 100 % / Method: Blot for 3-4 seconds before plunging
Time resolved state: Vitrified 30 msec after spraying with effector

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Mar 3, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 59000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 6 / Applied symmetry: C1 (asymmetric) / Number of projections: 57435
Details: The particles were selected using a semi-automated procedure in RELION.
3D reconstructionAlgorithm: Cross-common lines / Software: RELION / CTF correction: Each micrograph / Resolution: 8.7 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 4JSP

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