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- EMDB-3560: mitochondrial ATP synthase dimer from Trypanosoma brucei -

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Basic information

Entry
Database: EMDB / ID: EMD-3560
Titlemitochondrial ATP synthase dimer from Trypanosoma brucei
Map datasubtomogram average of mitochondrial ATP synthase dimer from Trypanosoma brucei
Sample
  • Organelle or cellular component: ATP synthase dimer from Trypanosoma brucei in isolated mitochondrial membranes
Biological speciesTrypanosoma brucei (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 32.5 Å
AuthorsMuehleip AW / Kuehlbrandt W / Davies KM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: In situ structure of trypanosomal ATP synthase dimer reveals a unique arrangement of catalytic subunits.
Authors: Alexander W Mühleip / Caroline E Dewar / Achim Schnaufer / Werner Kühlbrandt / Karen M Davies /
Abstract: We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma ...We used electron cryotomography and subtomogram averaging to determine the in situ structures of mitochondrial ATP synthase dimers from two organisms belonging to the phylum euglenozoa: Trypanosoma brucei, a lethal human parasite, and Euglena gracilis, a photosynthetic protist. At a resolution of 32.5 Å and 27.5 Å, respectively, the two structures clearly exhibit a noncanonical F head, in which the catalytic (αβ) assembly forms a triangular pyramid rather than the pseudo-sixfold ring arrangement typical of all other ATP synthases investigated so far. Fitting of known X-ray structures reveals that this unusual geometry results from a phylum-specific cleavage of the α subunit, in which the C-terminal α fragments are displaced by ∼20 Å and rotated by ∼30° from their expected positions. In this location, the α fragment is unable to form the conserved catalytic interface that was thought to be essential for ATP synthesis, and cannot convert γ-subunit rotation into the conformational changes implicit in rotary catalysis. The new arrangement of catalytic subunits suggests that the mechanism of ATP generation by rotary ATPases is less strictly conserved than has been generally assumed. The ATP synthases of these organisms present a unique model system for discerning the individual contributions of the α and β subunits to the fundamental process of ATP synthesis.
History
DepositionDec 26, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateAug 30, 2017-
Current statusAug 30, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 154
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 154
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3560.png

Downloads & links

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Map

FileDownload / File: emd_3560.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsubtomogram average of mitochondrial ATP synthase dimer from Trypanosoma brucei
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.69 Å/pix.
x 110 pix.
= 736.23 Å		6.69 Å/pix.
x 110 pix.
= 736.23 Å		6.69 Å/pix.
x 110 pix.
= 736.23 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 154. / Movie #1: 154
Minimum - Maximum138.021320000000003 - 166.352309999999989
Average (Standard dev.)149.420350000000013 (±1.1904656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 736.23 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.6936.6936.693
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z736.230736.230736.230
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean138.021166.352149.420

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Supplemental data

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Sample components

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Entire : ATP synthase dimer from Trypanosoma brucei in isolated mitochondr...

EntireName: ATP synthase dimer from Trypanosoma brucei in isolated mitochondrial membranes
Components
  • Organelle or cellular component: ATP synthase dimer from Trypanosoma brucei in isolated mitochondrial membranes

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Supramolecule #1: ATP synthase dimer from Trypanosoma brucei in isolated mitochondr...

SupramoleculeName: ATP synthase dimer from Trypanosoma brucei in isolated mitochondrial membranes
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Trypanosoma brucei (eukaryote) / Strain: 29.13 / Organelle: mitochondria
Molecular weightTheoretical: 2 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTristris(hydroxymethyl)aminomethane
250.0 mMtrehalose
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Average electron dose: 1.6 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 defocus max: 4.0 µm / Nominal defocus min: 3.5 µm / Nominal magnification: 42000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 32.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software: (Name: IMOD, PEET) / Number subtomograms used: 925
ExtractionNumber tomograms: 6 / Number images used: 925 / Reference model: crude average from original data / Method: volumes picked interactively / Software: (Name: 3dmod, IMOD)
CTF correctionSoftware - Name: IMOD / Details: strip-based method
Final angle assignmentType: OTHER / Software: (Name: IMOD, PEET)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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