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- EMDB-7036: Cryo-EM structure of the dimeric FO region of yeast mitochondrial... -

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Basic information

Entry
Database: EMDB / ID: 7036
TitleCryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
Map dataSharpened map of the dimeric FO region of yeast mitochondrial ATP synthase
SampleYeast mitochondrial ATP synthase FO complex:
(ATP synthase subunit ...) x 9 / ATP synthase protein 8
Function / homologyATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A, active site / ATP synthase subunit K / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase, F0 complex, subunit B / ATP synthase protein 8, fungi / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 ...ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F0 complex, subunit C / ATP synthase, F0 complex, subunit A, active site / ATP synthase subunit K / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase, F0 complex, subunit B / ATP synthase protein 8, fungi / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit J / V-ATPase proteolipid subunit C-like domain / ATP synthase, F0 complex, subunit A / F1F0 ATP synthase subunit C superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase A chain / ATP synthase subunit C / ATP synthase j chain / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase D chain, mitochondrial (ATP5H) / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / Protein of unknown function (DUF2611) / ATP synthase a subunit signature. / ATP synthase c subunit signature. / ATP synthase, F0 complex, subunit A superfamily / go:0035786: / mitochondrial proton-transporting ATP synthase complex assembly / ATP hydrolysis coupled cation transmembrane transport / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton transmembrane transporter activity / ATP hydrolysis coupled proton transport / ATP synthesis coupled proton transport / mitochondrial intermembrane space / mitochondrial inner membrane / protein complex oligomerization / lipid binding / integral component of membrane / identical protein binding / cytosol / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit K, mitochondrial / ATP synthase subunit f, mitochondrial
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
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.
Validation ReportPDB-ID: 6b2z

SummaryFull reportAbout validation report
DateDeposition: Sep 20, 2017 / Header (metadata) release: Nov 8, 2017 / Map release: Nov 8, 2017 / Last update: Nov 29, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6b2z
  • Surface level: 0.19
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7036.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
1.06 Å/pix.
= 339.2 Å
320 pix
1.06 Å/pix.
= 339.2 Å
320 pix
1.06 Å/pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.165 (by author), 0.19 (movie #1):
Minimum - Maximum-0.7367223 - 1.1907687
Average (Standard dev.)0.0009854478 (0.03345717)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.7371.1910.001

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Supplemental data

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Mask #1

Fileemd_7036_msk_1.map ( map file in CCP4 format, 131073 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsMask used for calculating FSC of the dimeric FO region of yeast mitochondrial ATP synthase
Space group number1

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Mask #1~

Fileemd_7036_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Yeast mitochondrial ATP synthase FO complex

EntireName: Yeast mitochondrial ATP synthase FO complex / Number of components: 11
MassTheoretical: 400 kDa

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Component #1: protein, Yeast mitochondrial ATP synthase FO complex

ProteinName: Yeast mitochondrial ATP synthase FO complex / Recombinant expression: No
MassTheoretical: 400 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A
Source (natural)Organelle: Mitochondria / Location in cell: Inner membrane of mitochondria

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Component #2: protein, ATP synthase subunit c, mitochondrial

ProteinName: ATP synthase subunit c, mitochondrial / Recombinant expression: No
MassTheoretical: 7.762375 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #3: protein, ATP synthase protein 8

ProteinName: ATP synthase protein 8 / Recombinant expression: No
MassTheoretical: 5.825215 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #4: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Recombinant expression: No
MassTheoretical: 27.90043 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #5: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Recombinant expression: No
MassTheoretical: 23.194498 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A

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Component #6: protein, ATP synthase subunit d, mitochondrial

ProteinName: ATP synthase subunit d, mitochondrial / Recombinant expression: No
MassTheoretical: 19.709424 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #7: protein, ATP synthase subunit e, mitochondrial

ProteinName: ATP synthase subunit e, mitochondrial / Recombinant expression: No
MassTheoretical: 4.188154 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #8: protein, ATP synthase subunit f, mitochondrial

ProteinName: ATP synthase subunit f, mitochondrial / Recombinant expression: No
MassTheoretical: 10.584166 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #9: protein, ATP synthase subunit g

ProteinName: ATP synthase subunit g / Recombinant expression: No
MassTheoretical: 9.039134 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A

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Component #10: protein, ATP synthase subunit j, mitochondrial

ProteinName: ATP synthase subunit j, mitochondrial / Recombinant expression: No
MassTheoretical: 6.696771 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Component #11: protein, ATP synthase subunit k, mitochondrial

ProteinName: ATP synthase subunit k, mitochondrial / Recombinant expression: No
MassTheoretical: 7.546778 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Temperature: 277 K / Humidity: 100 % / Details: blot for 26 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 71 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000 X (nominal), 47170 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm / Energy window: 0-20 eV
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 3023

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 238848
3D reconstructionSoftware: cryoSPARC / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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