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- EMDB-3169: Bovine mitochondrial ATP synthase state 3a -

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Basic information

Entry
Database: EMDB / ID: EMD-3169
TitleBovine mitochondrial ATP synthase state 3a
Map data
SampleBovine mitochondrial ATP synthase:
ATP synthase
KeywordsATP synthase / rotary ATPase
Function / homology
Function and homology information


proton-transporting ATP synthase complex / 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 envelope / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / ATP biosynthetic process / proton transmembrane transport / mitochondrial ATP synthesis coupled proton transport ...proton-transporting ATP synthase complex / 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 envelope / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / ATP biosynthetic process / proton transmembrane transport / mitochondrial ATP synthesis coupled proton transport / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase complex, catalytic core F(1) / ATP synthesis coupled proton transport / proton transmembrane transporter activity / H+-transporting two-sector ATPase / aerobic respiration / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial inner membrane / lipid binding / ATPase / integral component of membrane / ATP binding / plasma membrane
ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F0 complex, subunit D, mitochondrial / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, beta subunit ...ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F0 complex, subunit D, mitochondrial / ATPase, OSCP/delta subunit / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, delta/epsilon subunit / V-ATPase proteolipid subunit C-like domain / AAA+ ATPase domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, beta subunit / ATP synthase-coupling factor 6, mitochondrial / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / ATP synthase, F0 complex, subunit C / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / ATPase, OSCP/delta subunit, conserved site / ATP synthase, F0 complex, subunit A, active site / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATP synthase, F1 complex, gamma subunit conserved site / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / P-loop containing nucleoside triphosphate hydrolase / ATP synthase, F0 complex, subunit A / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase, F0 complex, subunit A superfamily / ATP synthase-coupling factor 6 superfamily, mitochondrial / F1F0 ATP synthase subunit C superfamily / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / ATP synthase, F1 complex, gamma subunit / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / F/V-ATP synthase subunit C superfamily / ATP synthase, F1 complex, gamma subunit superfamily
ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit beta, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit a / ATP synthase F(0) complex subunit C1, mitochondrial
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.4 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.
Validation ReportSummary, Full report, XML, About validation report
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-5fik
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5fik
  • Surface level: 0.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3169.tif

Downloads & links

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Map

FileDownload / File: emd_3169.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 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-0.09424381 - 0.51472884
Average (Standard dev.)-0.00061667 (±0.02213132)
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-0.0940.515-0.001

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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 / Details: Detergent-solubilized protein complex / Number of components: 1
Oligomeric State: One hetero-oligomeric ATP synthase complex
MassExperimental: 600 kDa

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Component #1: protein, ATP synthase

ProteinName: ATP synthase / a.k.a: ATPase, complex V / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 1
MassExperimental: 600 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organelle: Mitochondria / Location in cell: Mitochondrial membrane / Organ or tissue: Heart

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 8 mg/mL
Buffer solution: 20 mM Tris-HCl, 100 mM NaCl, 0.05% (wt/v) dodecylmaltoside, 2 mM ATP, 0.02% (wt/v) NaN3
pH: 7.2
Support filmHomemade holey carbon on 400 square mesh Cu/Rh grid, glow-discharged 2 mins
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE-PROPANE MIXTURE / Humidity: 100 % / Method: Blot for 27 seconds before plunging

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Electron microscopy imaging #1

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Mar 15, 2015
Details: K2 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 ...Details: K2 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.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60.3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000 X (nominal), 30487 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification)
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4100 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80
CameraDetector: GATAN K2 (4k x 4k)

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Electron microscopy imaging #2

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Sep 28, 2014
Details: K2 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 ...Details: K2 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.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60.3 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000 X (nominal), 30487 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 18,000x magnification (before detector post-magnification)
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 4100 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 80
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5867 / Sampling size: 5 µm / Bit depth: 8

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 24140
Details: The particles were selected using an automatic selection program.
3D reconstructionAlgorithm: Projection matching and maximum likelihood classification
Software: Relion, FREALIGN / CTF correction: Each particle
Details: To avoid noise bias, only data up to a resolution of 10 angstrom were used during refinement.
Resolution: 6.4 Å / Resolution method: FSC 0.143, semi-independent

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Atomic model buiding

Modeling #1Software: Chimera, MDFF / Refinement protocol: flexible / Refinement space: REAL
Details: Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
Input PDB model: 2WSS

2wss


Chain ID: A, B, C, D, E, F, G, H, I, S
Modeling #2Software: Chimera, MDFF / Refinement protocol: flexible / Refinement space: REAL
Details: Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
Input PDB model: 2XND

2xnd


Chain ID: J, K, L, M, N, O, P, Q
Modeling #3Software: Chimera, MDFF / Refinement protocol: flexible / Refinement space: REAL
Details: Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
Input PDB model: 2CLY

2cly


Chain ID: D, E, F
Output model

5fik

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