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- EMDB-2161: Structure of the yeast F1Fo-ATP synthase dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-2161
TitleStructure of the yeast F1Fo-ATP synthase dimer
Map dataSubtomgram average of Yeast ATP synthase dimers in mitochondrial membranes
Sample
  • Sample: ATP synthase dimer from mitochondria of Saccharomyces cerevisiae
  • Organelle or cellular component: F1Fo-ATP synthase
KeywordsMitochondria / Subtomogram average
Function / homology
Function and homology information


: / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / : / : / proton-transporting ATP synthase complex / : / : / : ...: / Formation of ATP by chemiosmotic coupling / Cristae formation / Mitochondrial protein degradation / : / : / proton-transporting ATP synthase complex / : / : / : / Mitochondrial protein degradation / mitochondrial nucleoid / 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 / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / 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) ...: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / 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, 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 / 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-coupling factor 6, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae W303 (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 37.0 Å
AuthorsDavies KM / Kuehlbrandt W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae.
Authors: Karen M Davies / Claudio Anselmi / Ilka Wittig / José D Faraldo-Gómez / Werner Kühlbrandt /
Abstract: We used electron cryotomography of mitochondrial membranes from wild-type and mutant Saccharomyces cerevisiae to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram ...We used electron cryotomography of mitochondrial membranes from wild-type and mutant Saccharomyces cerevisiae to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram averaging of the dimers to 3.7 nm resolution revealed a V-shaped structure of twofold symmetry, with an angle of 86° between monomers. The central and peripheral stalks are well resolved. The monomers interact within the membrane at the base of the peripheral stalks. In wild-type mitochondria ATP synthase dimers are found in rows along the highly curved cristae ridges, and appear to be crucial for membrane morphology. Strains deficient in the dimer-specific subunits e and g or the first transmembrane helix of subunit 4 lack both dimers and lamellar cristae. Instead, cristae are either absent or balloon-shaped, with ATP synthase monomers distributed randomly in the membrane. Computer simulations indicate that isolated dimers induce a plastic deformation in the lipid bilayer, which is partially relieved by their side-by-side association. We propose that the assembly of ATP synthase dimer rows is driven by the reduction in the membrane elastic energy, rather than by direct protein contacts, and that the dimer rows enable the formation of highly curved ridges in mitochondrial cristae.
History
DepositionJul 17, 2012-
Header (metadata) releaseAug 15, 2012-
Map releaseAug 15, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 7.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4b2q
  • Surface level: 7.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2161.png

emd_2161.png

Downloads & links

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Map

FileDownload / File: emd_2161.map.gz / Format: CCP4 / Size: 619.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomgram average of Yeast ATP synthase dimers in mitochondrial membranes
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.76 Å/pix.
x 60 pix.
= 345.6 Å		5.76 Å/pix.
x 30 pix.
= 172.8 Å		5.76 Å/pix.
x 90 pix.
= 518.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.7 / Movie #1: 7.7
Minimum - Maximum0.60975266 - 11.210791589999999
Average (Standard dev.)5.1059494 (±1.44749439)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions309060
Spacing309060
CellA: 518.4 Å / B: 172.8 Å / C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.765.765.76
M x/y/z903060
origin x/y/z0.0000.0000.000
length x/y/z518.400172.800345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS903060
D min/max/mean0.61011.2115.106

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Supplemental data

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Sample components

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Entire : ATP synthase dimer from mitochondria of Saccharomyces cerevisiae

EntireName: ATP synthase dimer from mitochondria of Saccharomyces cerevisiae
Components
  • Sample: ATP synthase dimer from mitochondria of Saccharomyces cerevisiae
  • Organelle or cellular component: F1Fo-ATP synthase

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Supramolecule #1000: ATP synthase dimer from mitochondria of Saccharomyces cerevisiae

SupramoleculeName: ATP synthase dimer from mitochondria of Saccharomyces cerevisiae
type: sample / ID: 1000
Details: Average of subvolumes extracted from tomograms of mitochondrial membrane fragments
Number unique components: 1
Molecular weightTheoretical: 1.2 MDa

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Supramolecule #1: F1Fo-ATP synthase

SupramoleculeName: F1Fo-ATP synthase / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Saccharomyces cerevisiae W303 (yeast) / Strain: W303 / Organelle: Mitochondria / Location in cell: Cristae membranes
Molecular weightTheoretical: 1.2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging

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Sample preparation

BufferpH: 7.4 / Details: 250mM Trehalose, 10nm Tris-HCl pH7.4
GridDetails: 300 mesh copper grid with quantifoil support film (R2/2), glow discharged
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER / Method: Single side manual blotting for 5 seconds.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: Standard procedure
Specialist opticsEnergy filter - Name: GIF Tridiem 863 / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateMar 11, 2009
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 160 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 24500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 7.0 µm / Nominal magnification: 41000
Sample stageSpecimen holder model: OTHER / Tilt series - Axis1 - Min angle: -50 ° / Tilt series - Axis1 - Max angle: 60 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsTomogram reconstruction performed in IMOD. Average number of tilts used in the 3D reconstructions: 75. Average tomographic tilt angle increment: 1.5.
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMOD / Details: Final map calculated from 121 subvolumes

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Atomic model buiding 1

Initial modelPDB ID:

2wpd


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: J / Chain - #10 - Chain ID: K / Chain - #11 - Chain ID: L / Chain - #12 - Chain ID: M / Chain - #13 - Chain ID: N / Chain - #14 - Chain ID: O / Chain - #15 - Chain ID: P / Chain - #16 - Chain ID: Q / Chain - #17 - Chain ID: R / Chain - #18 - Chain ID: S
SoftwareName: Chimera
DetailsProtocol: Rigid body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4b2q:
Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average

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Atomic model buiding 2

Initial modelPDB ID:

2cly


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera
DetailsProtocol: Rigid body with sequential fit command. Chain A extended using residues 180-207 of chain T from 2WSS
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4b2q:
Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average

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Atomic model buiding 3

Initial modelPDB ID:

2bo5


Chain - Chain ID: A
SoftwareName: Chimera
DetailsProtocol: Rigid body with sequential fit command
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4b2q:
Model of the yeast F1Fo-ATP synthase dimer based on subtomogram average

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