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- EMDB-3166: Bovine mitochondrial ATP synthase state 2a -

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Basic information

Entry
Database: EMDB / ID: EMD-3166
TitleBovine mitochondrial ATP synthase state 2a
Map dataReconstruction of detergent-solubilized bovine mitochondrial ATP synthase
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 channel activity / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain ...Mitochondrial protein import / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / proton channel activity / Mitochondrial protein degradation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / ADP binding / mitochondrial membrane / mitochondrial inner membrane / lipid binding / structural molecule activity / 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, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / 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 F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(0) complex subunit a / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 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
DepositionSep 24, 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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.13
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5arh
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5arh
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3166.tif

EMDB-3166.tif

Downloads & links

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Map

FileDownload / File: emd_3166.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of detergent-solubilized bovine mitochondrial ATP synthase
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-0.09678332 - 0.46938631
Average (Standard dev.)-0.00024286 (±0.02186722)
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-0.0970.469-0.000

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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 / Details: Detergent-solubilized protein complex
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 (domestic 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

DetailsThe particles were selected using an automatic selection program.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: OTHER / Software - Name: Relion, FREALIGN
Details: To avoid noise bias, only data up to a resolution of 10 angstrom were used during refinement.
Number images used: 19250

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Atomic model buiding 1

Initial modelPDB ID:

2wss


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F / Chain - #6 - Chain ID: G / Chain - #7 - Chain ID: H / Chain - #8 - Chain ID: I / Chain - #9 - Chain ID: S
SoftwareName: Chimera, MDFF
DetailsRigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5arh:
Bovine mitochondrial ATP synthase state 2a

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Atomic model buiding 2

Initial modelPDB ID:

2xnd


Chain - #0 - Chain ID: J / Chain - #1 - Chain ID: K / Chain - #2 - Chain ID: L / Chain - #3 - Chain ID: M / Chain - #4 - Chain ID: N / Chain - #5 - Chain ID: O / Chain - #6 - Chain ID: P / Chain - #7 - Chain ID: Q
SoftwareName: Chimera, MDFF
DetailsRigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5arh:
Bovine mitochondrial ATP synthase state 2a

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Atomic model buiding 3

Initial modelPDB ID:

2cly


Chain - #0 - Chain ID: D / Chain - #1 - Chain ID: E / Chain - #2 - Chain ID: F
SoftwareName: Chimera, MDFF
DetailsRigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-5arh:
Bovine mitochondrial ATP synthase state 2a

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