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- EMDB-7037: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -

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Basic information

Entry
Database: EMDB / ID: EMD-7037
TitleCryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase with C1 symmetry
Map dataSharpened map of dimeric FO region of yeast mitochondrial ATP synthase
Sample
  • Complex: Yeast mitochondrial ATP synthase FO complex
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGuo H / Rubinstein JL
CitationJournal: Science / Year: 2017
Title: Atomic model for the dimeric F region of mitochondrial ATP synthase.
Authors: Hui Guo / Stephanie A Bueler / John L Rubinstein /
Abstract: Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic ...Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F region turns the rotor that drives ATP synthesis in the soluble F region. Although crystal structures of the F region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F region. Using cryo-electron microscopy, we determined the structure of the dimeric F complex from at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae.
History
DepositionSep 21, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 8, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7037.png

Downloads & links

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Map

FileDownload / File: emd_7037.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of dimeric FO region of yeast mitochondrial ATP synthase
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.162 / Movie #1: 0.18
Minimum - Maximum-0.5518356 - 0.88963765
Average (Standard dev.)0.0009859481 (±0.028941598)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z339.200339.200339.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.5520.8900.001

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Supplemental data

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Mask #1

Fileemd_7037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of dimeric FO region of yeast...

Fileemd_7037_additional.map
AnnotationUnsharpened map of dimeric FO region of yeast mitochondrial ATP synthase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Dimeric FO region of yeast mitochondrial ATP synthase, half map-1

Fileemd_7037_half_map_1.map
AnnotationDimeric FO region of yeast mitochondrial ATP synthase, half map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Dimeric FO region of yeast mitochondrial ATP synthase, half map-2

Fileemd_7037_half_map_2.map
AnnotationDimeric FO region of yeast mitochondrial ATP synthase, half map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Yeast mitochondrial ATP synthase FO complex

EntireName: Yeast mitochondrial ATP synthase FO complex
Components
  • Complex: Yeast mitochondrial ATP synthase FO complex

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Supramolecule #1: Yeast mitochondrial ATP synthase FO complex

SupramoleculeName: Yeast mitochondrial ATP synthase FO complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1A
Molecular weightTheoretical: 400 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 7.4
GridModel: Homemade / Material: COPPER/RHODIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Details: blot for 26 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 2 / Number real images: 3023 / Average exposure time: 10.0 sec. / Average electron dose: 71.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 446259
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: Starting model generated by ab initio 3D reconstruction with cryoSPARC.
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.4.1) / Number images used: 238848

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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