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- EMDB-65574: In situ structure of mitochondrial ATP synthase in whole C. reinh... -

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Basic information

Entry
Database: EMDB / ID: EMD-65574
TitleIn situ structure of mitochondrial ATP synthase in whole C. reinhardtii cells
Map data
Sample
  • Cell: In situ mitochonrdial ATP synthase dimer for C. reinhardtii
KeywordsATP synthase / MEMBRANE PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 8.9 Å
AuthorsLuo ZW / Wang QH / Ma JP
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: OPUS-TOMO: Towards Resolving Dynamics and Compositional Heterogeneities of Biomolecules with Cryo-Electron Tomography
Authors: Luo ZW / Wang QH / Ma JP
History
DepositionJul 28, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65574.png

Downloads & links

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Map

FileDownload / File: emd_65574.map.gz / Format: CCP4 / Size: 132.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 326 pix.
= 638.96 Å		1.96 Å/pix.
x 326 pix.
= 638.96 Å		1.96 Å/pix.
x 326 pix.
= 638.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.0117558995 - 0.039790027
Average (Standard dev.)0.00019599739 (±0.0030206265)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions326326326
Spacing326326326
CellA=B=C: 638.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_65574_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: #1

Fileemd_65574_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65574_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ mitochonrdial ATP synthase dimer for C. reinhardtii

EntireName: In situ mitochonrdial ATP synthase dimer for C. reinhardtii
Components
  • Cell: In situ mitochonrdial ATP synthase dimer for C. reinhardtii

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Supramolecule #1: In situ mitochonrdial ATP synthase dimer for C. reinhardtii

SupramoleculeName: In situ mitochonrdial ATP synthase dimer for C. reinhardtii
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 3.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / 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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: M / Number subtomograms used: 47690
ExtractionNumber tomograms: 261 / Number images used: 78300 / Method: Template Matching / Software - Name: Warp
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: M
FSC plot (resolution estimation)

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