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- EMDB-10475: Cryo-EM structure of the Euglena gracilis mitochondrial ATP synth... -

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Basic information

Entry
Database: EMDB / ID: EMD-10475
TitleCryo-EM structure of the Euglena gracilis mitochondrial ATP synthase, OSCP/F1/c-ring, rotational state 3 without IF1
Map data
Sample
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer
Biological speciesEuglena gracilis (euglena)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsMuhleip A / Amunts A
CitationJournal: Elife / Year: 2019
Title: Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Authors: Alexander Mühleip / Sarah E McComas / Alexey Amunts /
Abstract: The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum ...The mitochondrial ATP synthase fuels eukaryotic cells with chemical energy. Here we report the cryo-EM structure of a divergent ATP synthase dimer from mitochondria of , a member of the phylum Euglenozoa that also includes human parasites. It features 29 different subunits, 8 of which are newly identified. The membrane region was determined to 2.8 Å resolution, enabling the identification of 37 associated lipids, including 25 cardiolipins, which provides insight into protein-lipid interactions and their functional roles. The rotor-stator interface comprises four membrane-embedded horizontal helices, including a distinct subunit . The dimer interface is formed entirely by phylum-specific components, and a peripherally associated subcomplex contributes to the membrane curvature. The central and peripheral stalks directly interact with each other. Last, the ATPase inhibitory factor 1 (IF) binds in a mode that is different from human, but conserved in Trypanosomatids.
History
DepositionNov 10, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseNov 27, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10475.png

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Map

FileDownload / File: emd_10475.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å		1.05 Å/pix.
x 440 pix.
= 462. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
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Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.029944621 - 0.065882795
Average (Standard dev.)0.00028315373 (±0.0022358142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 461.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z462.000462.000462.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.0300.0660.000

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Supplemental data

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Mask #1

Fileemd_10475_msk_1.map
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Additional map: unsharpened full map

Fileemd_10475_additional.map
Annotationunsharpened full map
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Additional map: unsharpened full map

Fileemd_10475_additional_1.map
Annotationunsharpened full map
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Half map: #1

Fileemd_10475_half_map_1.map
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Half map: #2

Fileemd_10475_half_map_2.map
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Sample components

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Entire : Euglena gracilis mitochondrial ATP synthase dimer

EntireName: Euglena gracilis mitochondrial ATP synthase dimer
Components
  • Complex: Euglena gracilis mitochondrial ATP synthase dimer

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Supramolecule #1: Euglena gracilis mitochondrial ATP synthase dimer

SupramoleculeName: Euglena gracilis mitochondrial ATP synthase dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#29
Source (natural)Organism: Euglena gracilis (euglena)
Molecular weightTheoretical: 2 MDa

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 5 seconds blot.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 9045 / Average exposure time: 10.0 sec. / Average electron dose: 36.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 555269
CTF correctionSoftware - Name: RELION
Startup modelType of model: EMDB MAP
EMDB ID:

3559

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28922
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 2 / Software - Name: RELION
FSC plot (resolution estimation)

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