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- EMDB-3181: Average of seven maps of the bovine mitochondrial ATP synthase wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-3181
TitleAverage of seven maps of the bovine mitochondrial ATP synthase with Fo regions aligned
Map dataAverage of seven maps of the bovine ATP synthase with their Fo regions aligned
Sample
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: ATP synthase
KeywordsATP synthase / rotary ATPase
Function / homology
Function and homology information


Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / : / : / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton motive force-driven mitochondrial 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-transporting ATP synthase activity, rotational mechanism / aerobic respiration / proton transmembrane transport / ADP binding / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / plasma membrane
Similarity search - Function
ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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 / C-terminal domain of V and A type ATP synthase / 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 subunit beta, mitochondrial / ATP synthase subunit a / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsZhou A / Rohou A / Schep DG / Bason JV / Montgomery MG / Walker JE / Grigorieff N / Rubinstein JL
CitationJournal: Elife / Year: 2015
Title: Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.
Authors: Anna Zhou / Alexis Rohou / Daniel G Schep / John V Bason / Martin G Montgomery / John E Walker / Nikolaus Grigorieff / John L Rubinstein /
Abstract: Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic ...Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.
History
DepositionOct 2, 2015-
Header (metadata) releaseOct 14, 2015-
Map releaseOct 14, 2015-
UpdateMar 30, 2016-
Current statusMar 30, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3181.tif

Downloads & links

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Map

FileDownload / File: emd_3181.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAverage of seven maps of the bovine ATP synthase with their Fo regions aligned
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 256 pix.
= 419.84 Å		1.64 Å/pix.
x 256 pix.
= 419.84 Å		1.64 Å/pix.
x 256 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13 / Movie #1: 0.13
Minimum - Maximum-0.07169441 - 0.38746077
Average (Standard dev.)-0.0004466 (±0.01956162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z419.840419.840419.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0720.387-0.000

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Supplemental data

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Sample components

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Entire : Bovine mitochondrial ATP synthase

EntireName: Bovine mitochondrial ATP synthase
Components
  • Sample: Bovine mitochondrial ATP synthase
  • Protein or peptide: ATP synthase

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Supramolecule #1000: Bovine mitochondrial ATP synthase

SupramoleculeName: Bovine mitochondrial ATP synthase / type: sample / ID: 1000
Oligomeric state: One hetero-oligomeric ATP synthase complex
Number unique components: 1
Molecular weightExperimental: 600 KDa

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Macromolecule #1: ATP synthase

MacromoleculeName: ATP synthase / type: protein_or_peptide / ID: 1 / Name.synonym: ATPase, complex V / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: Heart / Organelle: Mitochondria / Location in cell: Mitochondrial membrane
Molecular weightExperimental: 600 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

Concentration8 mg/mL
BufferpH: 7.2
Details: 20 mM Tris-HCl, 100 mM NaCl, 0.05% (wt/v) dodecylmaltoside, 2 mM ATP, 0.02% (wt/v) NaN3
GridDetails: Homemade holey carbon on 400 square mesh Cu/Rh grid, glow-discharged 2 mins
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 27 seconds before plunging

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification)
DetailsK2 Summit direct detector device (Gatan Inc.) operated in super-resolution mode with a 1.64 angstrom physical pixel and 0.82 angstrom super-resolution pixel. With no specimen present, the rate of exposure of the detector was 8 electrons/pixel/second. Exposure- fractionated movies of 20.1 s were recorded as stacks of 67 frames, so that selected specimen areas were exposed with a total of 60.3 electrons/square angstrom.
DateMar 15, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 5867 / Average electron dose: 60.3 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TITAN KRIOS
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification)
DetailsK2 Summit direct detector device (Gatan Inc.) operated in super-resolution mode with a 1.64 angstrom physical pixel and 0.82 angstrom super-resolution pixel. With no specimen present, the rate of exposure of the detector was 8 electrons/pixel/second. Exposure- fractionated movies of 20.1 s were recorded as stacks of 67 frames, so that selected specimen areas were exposed with a total of 60.3 electrons/square angstrom.
DateSep 28, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 5867 / Average electron dose: 60.3 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 30487 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.1 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsSeven refined maps were aligned and averaged in real space.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Relion, FREALIGN
Details: The resolution of this map was not determined because this map is a real space average of seven maps of the bovine ATP synthase aligned at their Fo region.
Number images used: 145055
Final two d classificationNumber classes: 7

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