|Entry||Database: EMDB / ID: 6399|
|Title||Structure of the intact ATM/Tel1 kinase|
|Map data||Reconstruction of ATM/Tel1|
|Sample||Endogenous ATM/Tel1 purified directly from the yeast cells:|
|Keywords||ATM/Tel1 / DSB / kinase activity|
|Source||Schizosaccharomyces pombe (fission yeast)|
|Method||single particle reconstruction / cryo EM / negative staining / 8.7 Å resolution|
|Authors||Wang XJ / Chu HY / Lv MJ / Zhang ZH / Qiu SW / Liu HY / Shen XT / Wang WW / Cai G|
|Citation||Journal: 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
|Date||Deposition: Jul 28, 2015 / Header (metadata) release: Nov 18, 2015 / Map release: Jul 27, 2016 / Last update: Jul 27, 2016|
|Structure viewer||EM map: |
Downloads & links
|File||emd_6399.map.gz (map file in CCP4 format, 65537 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.42 Å|
CCP4 map header:
-Entire Endogenous ATM/Tel1 purified directly from the yeast cells
|Entire||Name: Endogenous ATM/Tel1 purified directly from the yeast cells|
Number of components: 1
Oligomeric State: An asymmetric homo-dimeric architecture with pseudo C2 symmetry
|Mass||Theoretical: 700 kDa / Experimental: 700 kDa / Measured by: Sedimentation|
-Component #1: protein, ATM/Tel1
|Protein||Name: ATM/Tel1 / Oligomeric Details: Dimer / Recombinant expression: No / Number of Copies: 2|
|Mass||Theoretical: 700 kDa / Experimental: 700 kDa|
|Source||Species: Schizosaccharomyces pombe (fission yeast) / Strain: CC5060|
|Specimen||Specimen state: particle / Method: negative staining, cryo EM|
|Sample solution||Specimen 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
|Support film||a carbon-coated 400-mesh Cu EM specimen grid freshly glow discharged|
|Staining||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.|
|Vitrification||Instrument: 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
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS / Date: Mar 3, 2015|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 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 Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: 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 reconstruction||Algorithm: Cross-common lines / Software: RELION / CTF correction: Each micrograph / Resolution: 8.7 Å / Resolution method: FSC 0.143, gold-standard|
-Atomic model buiding
|Modeling #1||Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL|
Input PDB model: 4JSP
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