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- EMDB-9523: Human dimeric ATM kinase -

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Basic information

Entry
Database: EMDB / ID: 9523
TitleHuman dimeric ATM kinase
Map data
SampleHuman dimeric ATM kinase:
SourceHomo sapiens (human)
Methodsingle particle reconstruction / 24 Å resolution
AuthorsHuen MS / Lau WC
CitationJournal: To Be Published
Title: Structural characterization of the human ATM kinase
Authors: Lau WC / Li Y / Liu Z / Gao Y / Zhang Q / Huen MS
DateDeposition: Jul 9, 2016 / Header (metadata) release: Aug 8, 2018 / Map release: Aug 8, 2018 / Last update: Aug 8, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9523.map.gz (map file in CCP4 format, 4001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.61 Å/pix.
= 461. Å
100 pix
4.61 Å/pix.
= 461. Å
100 pix
4.61 Å/pix.
= 461. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.61 Å
Density
Contour Level:0.065 (by author), 0.065 (movie #1):
Minimum - Maximum-0.07670976 - 0.23108391
Average (Standard dev.)0.0005206233 (0.0143305)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin0.0.0.
Limit99.99.99.
Spacing100100100
CellA=B=C: 461.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.614.614.61
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z461.000461.000461.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.0770.2310.001

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Supplemental data

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Sample components

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Entire Human dimeric ATM kinase

EntireName: Human dimeric ATM kinase / Number of components: 1

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Component #1: protein, Human dimeric ATM kinase

ProteinName: Human dimeric ATM kinase / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pcDNA3.1(+)Flag-His-Atm wt

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionSpecimen conc.: 0.02 mg/ml / pH: 8
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6218
3D reconstructionResolution: 24 Å / Resolution method: FSC 0.143 CUT-OFF

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