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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: EMD-7036
TitleCryo-EM structure of the dimeric FO region of yeast mitochondrial ATP synthase
Map data
SampleYeast mitochondrial ATP synthase FO complex:
(ATP synthase subunit ...) x 9 / ATP synthase protein 8
Function / homology
Function and homology information


Cristae formation / Formation of ATP by chemiosmotic coupling / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / ATP synthesis coupled proton transport / proton-transporting ATP synthase complex, coupling factor F(o) / proton transmembrane transporter activity / mitochondrial intermembrane space ...Cristae formation / Formation of ATP by chemiosmotic coupling / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / ATP synthesis coupled proton transport / proton-transporting ATP synthase complex, coupling factor F(o) / proton transmembrane transporter activity / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / mitochondrion / integral component of membrane / identical protein binding / cytosol
Similarity search - Function
ATP synthase subunit K / ATP synthase subunit K / ATP synthase, F0 complex, subunit J / Mitochondrial F1-F0 ATP synthase subunit F of fungi / Fungal ATP synthase protein 8 (A6L) / ATP synthase j chain / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase protein 8, fungal type / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit B/MI25 ...ATP synthase subunit K / ATP synthase subunit K / ATP synthase, F0 complex, subunit J / Mitochondrial F1-F0 ATP synthase subunit F of fungi / Fungal ATP synthase protein 8 (A6L) / ATP synthase j chain / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase protein 8, fungal type / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase a subunit signature. / ATP synthase, F0 complex, subunit A superfamily / ATP synthase, F0 complex, subunit A, active site / ATP synthase A chain / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / V-ATPase proteolipid subunit C-like domain / ATP synthase subunit C / F/V-ATP synthase subunit C superfamily
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo H / Rubinstein JL
Funding support Canada, United States, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 81294 Canada
Simons Foundation349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
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 20, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 8, 2017-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

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

Downloads & links

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Map

FileDownload / File: emd_7036.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å
1.06 Å/pix.
x 320 pix.
= 339.2 Å
1.06 Å/pix.
x 320 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 LevelBy AUTHOR: 0.165 / Movie #1: 0.19
Minimum - Maximum-0.7367223 - 1.1907687
Average (Standard dev.)0.0009854478 (±0.03345717)
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-0.7371.1910.001

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Supplemental data

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Segmentation: #1

Fileemd_7036_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Half map A of the dimeric FO region...

Fileemd_7036_additional_1.map
AnnotationHalf map A of the dimeric FO region of yeast mitochondrial ATP synthase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Half map B of the dimeric FO region...

Fileemd_7036_additional_2.map
AnnotationHalf map B of the dimeric FO region of yeast mitochondrial ATP synthase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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

Fileemd_7036_additional_3.map
AnnotationUnsharpened map of the dimeric FO region of yeast mitochondrial ATP synthase
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

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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 / Number of Copies: 20 / Recombinant expression: No
MassTheoretical: 7.762375 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #3: protein, ATP synthase protein 8

ProteinName: ATP synthase protein 8 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 5.825215 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.90043 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Number of Copies: 2 / 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 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 19.709424 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: ATP synthase subunit e, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 4.188154 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: ATP synthase subunit f, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 10.584166 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, ATP synthase subunit g

ProteinName: ATP synthase subunit g / Number of Copies: 2 / 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 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.696771 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: ATP synthase subunit k, mitochondrial / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 7.546778 kDa
SourceSpecies: Baker's yeast (baker's 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: OTHER / 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: 130000.0 X (nominal), 47170.0 X (calibrated) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 1000.0 - 2000.0 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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