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

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Basic information

Entry
Database: EMDB / ID: EMD-3582
TitleATP synthase dimer from Tetrahymena thermophila
Map data
Sample
  • Complex: ATP synthase dimer
Biological speciesTetrahymena (eukaryote)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsDudkina NV / Chaban Y
CitationJournal: Biochim Biophys Acta / Year: 2014
Title: Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation.
Authors: Yuriy Chaban / Egbert J Boekema / Natalya V Dudkina /
Abstract: Oxidative phosphorylation (OXPHOS) is the main source of energy in eukaryotic cells. This process is performed by means of electron flow between four enzymes, of which three are proton pumps, in the ...Oxidative phosphorylation (OXPHOS) is the main source of energy in eukaryotic cells. This process is performed by means of electron flow between four enzymes, of which three are proton pumps, in the inner mitochondrial membrane. The energy accumulated in the proton gradient over the inner membrane is utilized for ATP synthesis by a fifth OXPHOS complex, ATP synthase. Four of the OXPHOS protein complexes associate into stable entities called respiratory supercomplexes. This review summarises the current view on the arrangement of the electron transport chain in mitochondrial cristae. The functional role of the supramolecular organisation of the OXPHOS system and the factors that stabilise such organisation are highlighted. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.
History
DepositionJan 27, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseMar 1, 2017-
UpdateJul 26, 2017-
Current statusJul 26, 2017Processing site: PDBe / Status: Released

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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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3582.png

Downloads & links

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Map

FileDownload / File: emd_3582.map.gz / Format: CCP4 / Size: 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.)
3.8 Å/pix.
x 128 pix.
= 486.4 Å		3.8 Å/pix.
x 128 pix.
= 486.4 Å		3.8 Å/pix.
x 128 pix.
= 486.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-9.337363 - 15.459020000000001
Average (Standard dev.)0.04933456 (±0.57700413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 486.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
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
Components
  • Complex: ATP synthase dimer

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Supramolecule #1: ATP synthase dimer

SupramoleculeName: ATP synthase dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena (eukaryote)
Molecular weightTheoretical: 600 kDa/nm

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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

BufferpH: 7
StainingType: NEGATIVE / Material: Uranyl acetate / Details: 2% water solution

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Electron microscopy

MicroscopeFEI/PHILIPS CM12
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Particle selectionNumber selected: 50000
CTF correctionSoftware: (Name: IMAGIC, EMAN, SPIDER)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 6000
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: IMAGIC

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