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

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Basic information

Entry
Database: EMDB / ID: EMD-6399
TitleStructure of the intact ATM/Tel1 kinase
Map dataReconstruction of ATM/Tel1
Sample
  • Sample: Endogenous ATM/Tel1 purified directly from the yeast cells
  • Protein or peptide: ATM/Tel1
KeywordsATM/Tel1 / DSB / kinase activity
Biological speciesSchizosaccharomyces pombe (fission yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 8.7 Å
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 /
Abstract: The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed ...The ataxia-telangiectasia mutated (ATM) protein is an apical kinase that orchestrates the multifaceted DNA-damage response. Normally, ATM kinase is in an inactive, homodimer form and is transformed into monomers upon activation. Besides a conserved kinase domain at the C terminus, ATM contains three other structural modules, referred to as FAT, FATC and N-terminal helical solenoid. Here we report the first cryo-EM structure of ATM kinase, which is an intact homodimeric ATM/Tel1 from Schizosaccharomyces pombe. We show that two monomers directly contact head-to-head through the FAT and kinase domains. The tandem N-terminal helical solenoid tightly packs against the FAT and kinase domains. The structure suggests that ATM/Tel1 dimer interface and the consecutive HEAT repeats inhibit the binding of kinase substrates and regulators by steric hindrance. Our study provides a structural framework for understanding the mechanisms of ATM/Tel1 regulation as well as the development of new therapeutic agents.
History
DepositionJul 28, 2015-
Header (metadata) releaseNov 18, 2015-
Map releaseJul 27, 2016-
UpdateJul 27, 2016-
Current statusJul 27, 2016Processing site: PDBj / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6399.tif

Downloads & links

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Map

FileDownload / File: emd_6399.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ATM/Tel1
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.067 / Movie #1: 0.067
Minimum - Maximum-0.0982672 - 0.25424597
Average (Standard dev.)0.00141853 (±0.01484582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 363.52 Å
α=β=γ: 90.0 °

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
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
Components
  • Sample: Endogenous ATM/Tel1 purified directly from the yeast cells
  • Protein or peptide: ATM/Tel1

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Supramolecule #1000: Endogenous ATM/Tel1 purified directly from the yeast cells

SupramoleculeName: Endogenous ATM/Tel1 purified directly from the yeast cells
type: sample / ID: 1000
Oligomeric state: An asymmetric homo-dimeric architecture with pseudo C2 symmetry
Number unique components: 1
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa / Method: Sedimentation

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Macromolecule #1: ATM/Tel1

MacromoleculeName: ATM/Tel1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast) / Strain: CC5060 / synonym: yeast
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.6
Details: 50mmol/L Tris, 100mmol/L ammonium sulfate, 10%(v/v) glycerol, 1mmol/L EDTA, 10umol/L ZnSO4, 0.02% NP-40, 10mmol/b-ME
StainingType: NEGATIVE
Details: Sample 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.
GridDetails: a carbon-coated 400-mesh Cu EM specimen grid freshly glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV
Timed resolved state: Vitrified 30 msec after spraying with effector
Method: Blot for 3-4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 150,000 times magnification
DateMar 3, 2015
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using a semi-automated procedure in RELION.
CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 57435
Final two d classificationNumber classes: 6

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Atomic model buiding 1

Initial modelPDB ID:

4jsp

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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