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- EMDB-9523: Human dimeric ATM kinase -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-9523
TitleHuman dimeric ATM kinase
Map data
Sample
  • Complex: Human dimeric ATM kinase
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
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
History
DepositionJul 9, 2016-
Header (metadata) releaseAug 8, 2018-
Map releaseAug 8, 2018-
UpdateAug 8, 2018-
Current statusAug 8, 2018Processing site: PDBj / Status: Released

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Structure visualization

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

emd_9523.png

Downloads & links

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Map

FileDownload / File: emd_9523.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.065 / Movie #1: 0.065
Minimum - Maximum-0.07670976 - 0.23108391
Average (Standard dev.)0.0005206233 (±0.0143305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 461.0 Å
α=β=γ: 90.0 °

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
Components
  • Complex: Human dimeric ATM kinase

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Supramolecule #1: Human dimeric ATM kinase

SupramoleculeName: Human dimeric ATM kinase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pcDNA3.1(+)Flag-His-Atm wt

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 2010
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 6218
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)

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