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- EMDB-3672: Open protomer of human ATM (Ataxia telangiectasia mutated) -

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Open data


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Basic information

Entry
Database: EMDB / ID: 3672
TitleOpen protomer of human ATM (Ataxia telangiectasia mutated)
SampleDimeric human ATM (Ataxia telangiectasia mutated) kinase
SourceHomo sapiens / human
Map dataOpen protomer of human ATM (Ataxia telangiectasia mutated)
Methodsingle particle reconstruction, at 5.7 A resolution
AuthorsBaretic D / Pollard HK
CitationSci Adv, 2017, 3, e1700933-e1700933

Sci Adv, 2017, 3, e1700933-e1700933 StrPapers
Structures of closed and open conformations of dimeric human ATM.
Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams

DateDeposition: Apr 13, 2017 / Header (metadata) release: Apr 26, 2017 / Map release: May 17, 2017 / Last update: Apr 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.026
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5np1
  • Surface level: 0.035
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3672.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.43 A/pix
= 429. A
300 pix
1.43 A/pix
= 429. A
300 pix
1.43 A/pix
= 429. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.43 A
Density
Contour Level:0.026 (by author), 0.026 (movie #1):
Minimum - Maximum-0.043189295 - 0.13658357
Average (Standard dev.)-1.5486896E-5 (0.0037900372)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin000
Limit299299299
Spacing300300300
CellA=B=C: 428.99997 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.431.431.43
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z429.000429.000429.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0430.137-0.000

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Supplemental data

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Sample components

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Entire Dimeric human ATM (Ataxia telangiectasia mutated) kinase

EntireName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Number of components: 2
MassExperimental: 705 kDa

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Component #1: cellular-component, Dimeric human ATM (Ataxia telangiectasia muta...

Cellular-componentName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Recombinant expression: No
MassExperimental: 705 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Homo sapiens / human / Vector: pDEST12.2-OriP / Cell of expression system: HEK293

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Component #2: protein, Serine-protein kinase ATM

ProteinName: Serine-protein kinase ATM / Recombinant expression: No
MassTheoretical: 352.393969 kDa
Source (engineered)Expression System: Homo sapiens / human / Vector: pDEST12.2-OriP / Cell of expression system: HEK293

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.6 mg/ml / pH: 8
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 %
Details: 3 uL sample/grid blotted for 12 s before plunge-freezing

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2.1 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 97902 X (nominal), 35714 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2500 - 4000 nm / Energy filter: GIF Quantum Energy Filter
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.15 - K)
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2720

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 60556
3D reconstructionSoftware: RELION / Resolution: 5.7 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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