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- EMDB-10526: Subtomogram average of ATP synthase dimer from Toxoplasma gondii ... -

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Basic information

Entry
Database: EMDB / ID: EMD-10526
TitleSubtomogram average of ATP synthase dimer from Toxoplasma gondii mitochondrial membranes
Map data
Sample
  • Complex: Toxoplasma gondii mitochondria ATP synthase dimer
Biological speciesToxoplasma gondii GT1 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
AuthorsMuhleip A / Amunts A
CitationJournal: Nat Commun / Year: 2021
Title: ATP synthase hexamer assemblies shape cristae of Toxoplasma mitochondria.
Authors: Alexander Mühleip / Rasmus Kock Flygaard / Jana Ovciarikova / Alice Lacombe / Paula Fernandes / Lilach Sheiner / Alexey Amunts /
Abstract: Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has ...Mitochondrial ATP synthase plays a key role in inducing membrane curvature to establish cristae. In Apicomplexa causing diseases such as malaria and toxoplasmosis, an unusual cristae morphology has been observed, but its structural basis is unknown. Here, we report that the apicomplexan ATP synthase assembles into cyclic hexamers, essential to shape their distinct cristae. Cryo-EM was used to determine the structure of the hexamer, which is held together by interactions between parasite-specific subunits in the lumenal region. Overall, we identified 17 apicomplexan-specific subunits, and a minimal and nuclear-encoded subunit-a. The hexamer consists of three dimers with an extensive dimer interface that includes bound cardiolipins and the inhibitor IF. Cryo-ET and subtomogram averaging revealed that hexamers arrange into ~20-megadalton pentagonal pyramids in the curved apical membrane regions. Knockout of the linker protein ATPTG11 resulted in the loss of pentagonal pyramids with concomitant aberrantly shaped cristae. Together, this demonstrates that the unique macromolecular arrangement is critical for the maintenance of cristae morphology in Apicomplexa.
History
DepositionDec 4, 2019-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10526.png

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Map

FileDownload / File: emd_10526.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.42 Å/pix.
x 100 pix.
= 442. Å		4.42 Å/pix.
x 100 pix.
= 442. Å		4.42 Å/pix.
x 100 pix.
= 442. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-2.4041276 - 3.068504
Average (Standard dev.)-2.1687896e-08 (±0.35894305)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 442.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.424.424.42
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z442.000442.000442.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-2.4043.069-0.000

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Supplemental data

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Mask #1

Fileemd_10526_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_10526_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_10526_half_map_2.map
Projections & Slices
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Sample components

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Entire : Toxoplasma gondii mitochondria ATP synthase dimer

EntireName: Toxoplasma gondii mitochondria ATP synthase dimer
Components
  • Complex: Toxoplasma gondii mitochondria ATP synthase dimer

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Supramolecule #1: Toxoplasma gondii mitochondria ATP synthase dimer

SupramoleculeName: Toxoplasma gondii mitochondria ATP synthase dimer / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Toxoplasma gondii GT1 (eukaryote)
Molecular weightTheoretical: 1.85 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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 3.0 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: 64000
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

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PEET / Number subtomograms used: 139
ExtractionNumber tomograms: 1 / Number images used: 139
CTF correctionSoftware - Name: IMOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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