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- EMDB-3441: Subtomogram average of the mitochondrial ATP synthase dimer from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-3441
TitleSubtomogram average of the mitochondrial ATP synthase dimer from the ciliate Paramecium tetraurelia
Map dataSubtomogram average of mitochondrial ATP synthase dimer from the ciliate Paramecium tetraurelia
Sample
  • Sample: Mitochondrial ATP synthase dimer from Paramecium tetraurelia
  • Protein or peptide: Mitochondrial F1FoATPase
KeywordsATP synthase dimers / mitochondria / ciliate
Biological speciesParamecium tetraurelia (eukaryote)
Methodelectron tomography / cryo EM / Resolution: 26.0 Å
AuthorsMuehleip AW / Kuehlbrandt W / Davies KM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: Helical arrays of U-shaped ATP synthase dimers form tubular cristae in ciliate mitochondria.
Authors: Alexander W Mühleip / Friederike Joos / Christoph Wigge / Achilleas S Frangakis / Werner Kühlbrandt / Karen M Davies /
Abstract: F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V- ...F1Fo-ATP synthases are universal energy-converting membrane protein complexes that synthesize ATP from ADP and inorganic phosphate. In mitochondria of yeast and mammals, the ATP synthase forms V-shaped dimers, which assemble into rows along the highly curved ridges of lamellar cristae. Using electron cryotomography and subtomogram averaging, we have determined the in situ structure and organization of the mitochondrial ATP synthase dimer of the ciliate Paramecium tetraurelia. The ATP synthase forms U-shaped dimers with parallel monomers. Each complex has a prominent intracrista domain, which links the c-ring of one monomer to the peripheral stalk of the other. Close interaction of intracrista domains in adjacent dimers results in the formation of helical ATP synthase dimer arrays, which differ from the loose dimer rows in all other organisms observed so far. The parameters of the helical arrays match those of the cristae tubes, suggesting the unique features of the P. tetraurelia ATP synthase are directly responsible for generating the helical tubular cristae. We conclude that despite major structural differences between ATP synthase dimers of ciliates and other eukaryotes, the formation of ATP synthase dimer rows is a universal feature of mitochondria and a fundamental determinant of cristae morphology.
History
DepositionJun 17, 2016-
Header (metadata) releaseJul 6, 2016-
Map releaseJul 6, 2016-
UpdateAug 10, 2016-
Current statusAug 10, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 151
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 151
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3441.tif

Downloads & links

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Map

FileDownload / File: emd_3441.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSubtomogram average of mitochondrial ATP synthase dimer from the ciliate Paramecium tetraurelia
Voxel sizeX=Y=Z: 4.46 Å
Density
Contour LevelBy AUTHOR: 151.0 / Movie #1: 151
Minimum - Maximum134.86489868000001 - 161.085083010000005
Average (Standard dev.)146.916961670000006 (±1.12564516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 624.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.464.464.46
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z624.400624.400624.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean134.865161.085146.917

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Supplemental data

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Sample components

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Entire : Mitochondrial ATP synthase dimer from Paramecium tetraurelia

EntireName: Mitochondrial ATP synthase dimer from Paramecium tetraurelia
Components
  • Sample: Mitochondrial ATP synthase dimer from Paramecium tetraurelia
  • Protein or peptide: Mitochondrial F1FoATPase

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Supramolecule #1000: Mitochondrial ATP synthase dimer from Paramecium tetraurelia

SupramoleculeName: Mitochondrial ATP synthase dimer from Paramecium tetraurelia
type: sample / ID: 1000 / Oligomeric state: dimer / Number unique components: 1
Molecular weightTheoretical: 1.2 MDa

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Macromolecule #1: Mitochondrial F1FoATPase

MacromoleculeName: Mitochondrial F1FoATPase / type: protein_or_peptide / ID: 1 / Name.synonym: Mitochondrial ATP synthase dimer / Number of copies: 1 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Paramecium tetraurelia (eukaryote) / Strain: d4-2 / Cell: single-celled organism / Organelle: mitochondrion / Location in cell: crista membrane
Molecular weightTheoretical: 1.2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 20 mM Tris, 250 mM trehalose
GridDetails: 300 mesh Quantifoil copper grid R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 10 % / Chamber temperature: 110 K / Instrument: OTHER
Method: manual blotting for 5-6 seconds with Whatman paper #4

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 64000
Specialist opticsEnergy filter - Name: GIF Quantum, Gatan / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 ° / Tilt series - Axis1 - Angle increment: 2 °
TemperatureMin: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 64,000 times magnification
DateJul 3, 2013
Image recordingCategory: CCD / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number real images: 720 / Average electron dose: 100 e/Å2 / Camera length: 19.3 / Bits/pixel: 32
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each projection, strip-based approach
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET
Details: Final subtomogram average was generated from 1244 subvolumes.
Number images used: 60
DetailsIMOD was used to align tilt series based on the position of gold fiducials, correct CTF on each projection image, and generate a tomographic volume using weighted back-projection. Subtomogram averaging was performed with PEET after initial estimate of rotations were calculated based on the orientation of particles relative to the membrane.

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Atomic model buiding 1

Initial modelPDB ID:

3zry


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
SoftwareName: Chimera
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient maximization

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Atomic model buiding 2

Initial modelPDB ID:

2wss


Chain - #0 - Chain ID: S / Chain - #1 - Chain ID: W
SoftwareName: Chimera
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: cross correlation coefficient maximization

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