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

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Basic information

Entry
Database: EMDB / ID: EMD-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
Sample
  • Complex: Yeast mitochondrial F1Fo ATP synthase dimer
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis ...mitochondrial proton-transporting ATP synthase, central stalk / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
ATP synthase subunit K / ATP synthase subunit K / ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain ...ATP synthase subunit K / ATP synthase subunit K / ATP synthase, F0 complex, subunit J / ATP synthase protein 8, fungal type / ATP synthase, F0 complex, subunit F, mitochondria, fungi / ATP synthase j chain / Fungal ATP synthase protein 8 (A6L) / Mitochondrial F1-F0 ATP synthase subunit F of fungi / : / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / 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. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase catalytic sector F1 epsilon subunit / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial ...ATP synthase catalytic sector F1 epsilon subunit / ATP synthase subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase protein 8 / ATP synthase subunit 4, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit 5, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit J, mitochondrial / ATP synthase subunit K, mitochondrial / ATP synthase subunit f, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsGuo H / Bueler SA / Rubinstein JL
Funding support Canada, United States, 3 items
OrganizationGrant numberCountry
Canadian Institutes of Health ResearchMOP 81294 Canada
Simons Foundation349247 United States
NIH National Institute of General Medical SciencesGM103310 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
DepositionOct 7, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 8, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.156
  • Imaged by UCSF Chimera
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  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7067.png

Downloads & links

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Map

FileDownload / File: emd_7067.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the dimeric FO region of yeast mitochondrial ATP synthase
Voxel sizeX=Y=Z: 1.45 Å
Density
Contour LevelBy AUTHOR: 0.156 / Movie #1: 0.156
Minimum - Maximum-0.37390116 - 1.1033652
Average (Standard dev.)0.0015192016 (-)
SymmetrySpace group: 0
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 464.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.451.451.45
M x/y/z320320320
origin x/y/z-60.548-61.810-114.135
length x/y/z464.000464.000464.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.3741.1030.002

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Supplemental data

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Mask #1

Fileemd_7067_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_7067_half_map_1.map
AnnotationHalf map A of the 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: Half map B of the dimeric FO region...

Fileemd_7067_half_map_2.map
AnnotationHalf map B of the 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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Sample components

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Entire : Yeast mitochondrial F1Fo ATP synthase dimer

EntireName: Yeast mitochondrial F1Fo ATP synthase dimer
Components
  • Complex: Yeast mitochondrial F1Fo ATP synthase dimer

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Supramolecule #1: Yeast mitochondrial F1Fo ATP synthase dimer

SupramoleculeName: Yeast mitochondrial F1Fo ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: W303-1A / Organelle: Mitochondria / Location in cell: Inner membrane of mitochondria
Molecular weightTheoretical: 1.2 MDa

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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

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

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated magnification: 34483 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 25000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-30 / Number real images: 626 / Average exposure time: 15.0 sec. / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 143294
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: Starting model generated by ab initial 3D reconstruction with cryoSPARC.
Initial angle assignmentType: OTHER
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.4.1) / Number images used: 79942

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6b8h:
Mosaic model of yeast mitochondrial ATP synthase monomer

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