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- EMDB-3582: ATP synthase dimer from Tetrahymena thermophila -

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Basic information

Entry
Database: EMDB / ID: 3582
TitleATP synthase dimer from Tetrahymena thermophila
SampleATP synthase dimer
SourceTetrahymena / eukaryote
Map data
Methodsingle particle reconstruction, at 20 A resolution
AuthorsDudkina NV / Chaban Y
CitationBiochim. Biophys. Acta, 2014, 1837, 418-426

Biochim. Biophys. Acta, 2014, 1837, 418-426 StrPapers
Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation.
Yuriy Chaban / Egbert J Boekema / Natalya V Dudkina

DateDeposition: Jan 27, 2017 / Header (metadata) release: Feb 22, 2017 / Map release: Mar 1, 2017 / Last update: Jan 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 0.1
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_3582.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
3.8 A/pix
= 486.4 A
128 pix
3.8 A/pix
= 486.4 A
128 pix
3.8 A/pix
= 486.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.8 A
Density
Contour Level:0.1 (by author), 0.1 (movie #1):
Minimum - Maximum-9.337363 - 15.45902
Average (Standard dev.)0.04933456 (0.57700413)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin-64-64-64
Limit636363
Spacing128128128
CellA=B=C: 486.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.83.83.8
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z486.400486.400486.400
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-9.33715.4590.049

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Supplemental data

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Sample components

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Entire ATP synthase dimer

EntireName: ATP synthase dimer / Number of components: 1

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Component #1: protein, ATP synthase dimer

ProteinName: ATP synthase dimer / Recombinant expression: No
SourceSpecies: Tetrahymena / eukaryote
Source (natural)Organelle: mitochondria

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7
Staining2% water solution
VitrificationCryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM12
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 40 e/A2 / 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: 6000
3D reconstructionResolution: 20 A / Resolution method: FSC 0.5 CUT-OFF

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