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- EMDB-7067: Cryo-EM structure of dimeric F1FO yeast mitochondrial ATP synthas... -

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Entry
Database: EMDB / ID: 7067
TitleCryo-EM structure of dimeric F1FO yeast mitochondrial ATP synthase with C2 symmetry
Map dataSharpened map of the dimeric FO region of yeast mitochondrial ATP synthase
SampleYeast mitochondrial F1Fo ATP synthase dimer:
Function / homologyATP synthase, F0 complex, subunit A, active site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase subunit K / ATPase, OSCP/delta subunit, conserved site / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain ...ATP synthase, F0 complex, subunit A, active site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase subunit K / ATPase, OSCP/delta subunit, conserved site / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / 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 / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F0 complex, subunit A superfamily / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase alpha/beta family, nucleotide-binding domain / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase alpha/beta chain, C terminal domain / ATP synthase / ATP synthase delta (OSCP) subunit / ATP synthase subunit C / ATP synthase A chain / F1F0 ATP synthase subunit C superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, alpha subunit, C-terminal domain superfamily / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase, F0 complex, subunit J / ATP synthase, F1 complex, beta subunit / Mitochondrial ATP synthase epsilon chain / ATP synthase j chain / ATP synthase c subunit signature. / ATP synthase a subunit signature. / ATP synthase delta (OSCP) subunit signature. / ATP synthase gamma subunit signature. / ATP synthase alpha and beta subunits signature. / Protein of unknown function (DUF2611) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / Fungal ATP synthase protein 8 (A6L) / ATP synthase, F1 complex, alpha subunit / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase alpha/beta family, beta-barrel domain / ATP synthase, F0 complex, subunit A / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / AAA+ ATPase domain / V-ATPase proteolipid subunit C-like domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, alpha subunit, C-terminal / ATPase, OSCP/delta subunit / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit C / ATP synthase, F1 complex, gamma subunit / go:0035786: / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase, catalytic core / ATP hydrolysis coupled cation transmembrane transport / mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transporter activity / proton-transporting ATPase activity, rotational mechanism / ATP hydrolysis coupled proton transport / H+-transporting two-sector ATPase / ATP synthesis coupled proton transport / mitochondrial nucleoid / mitochondrial intermembrane space / mitochondrial inner membrane / protein complex oligomerization / lipid binding / mitochondrion / integral component of membrane / ATP binding / identical protein binding / cytosol / ATP synthase subunit d, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit K, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 4, mitochondrial / ATP synthase protein 8 / ATP synthase subunit a / ATP synthase catalytic sector F1 epsilon subunit / ATP synthase subunit delta, mitochondrial
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 7.4 Å resolution
AuthorsGuo H / Bueler SA / 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: 6b8h

SummaryFull reportAbout validation report
DateDeposition: Oct 7, 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: 0.156
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.156
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6b8h
  • Surface level: 0.156
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
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Supplemental images

Downloads & links

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Map

Fileemd_7067.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
1.45 Å/pix.
= 464. Å
320 pix
1.45 Å/pix.
= 464. Å
320 pix
1.45 Å/pix.
= 464. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.45 Å
Density
Contour Level:0.156 (by author), 0.156 (movie #1):
Minimum - Maximum-0.38966855 - 1.1660678
Average (Standard dev.)0.0015191714 (0.040992577)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions320320320
Origin000
Limit319319319
Spacing320320320
CellA=B=C: 464 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z464.000464.000464.000
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-0.3901.1660.002

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Supplemental data

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Mask #1

Fileemd_7067_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 detailsDimeric FO region of yeast mitochondrial ATP synthase
Space group number1

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Mask #1~

Fileemd_7067_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 F1Fo ATP synthase dimer

EntireName: Yeast mitochondrial F1Fo ATP synthase dimer / Number of components: 1
MassTheoretical: 1.2 MDa

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Component #1: protein, Yeast mitochondrial F1Fo ATP synthase dimer

ProteinName: Yeast mitochondrial F1Fo ATP synthase dimer / Recombinant expression: No
MassTheoretical: 1.2 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: W303-1A
Source (natural)Organelle: Mitochondria / Location in cell: Inner membrane of mitochondria

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 25000 X (nominal), 34483 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 626

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 79942
3D reconstructionSoftware: cryoSPARC / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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