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- EMDB-55464: In-cell structure of chlL-deleted C.reinhardtii chloroplast F-ATPase -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-55464
TitleIn-cell structure of chlL-deleted C.reinhardtii chloroplast F-ATPase
Map data
Sample
  • Cell: Cell lamellae of chlL-deleted C.reinhardtii
KeywordsChloroplast / ATPase / photosynthesis / ELECTRON TRANSPORT
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 24.8 Å
AuthorsHou Z / Zhang P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust311427/Z/24/Z United Kingdom
CitationJournal: To Be Published
Title: Spatiotemporal biogenesis of thylakoid membranes in Chlamydomonas reinhardtii
Authors: Ge X / Hou Z / Qi M / Munoz P / Pawlak K / Dykes GF / Zhang Y / Harris J / Zhang J / Chen L / Dumoux M / Heebner J / Johnson GN / Nixon PJ / Zhang P / Liu L-N
History
DepositionOct 22, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55464.png

Downloads & links

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Map

FileDownload / File: emd_55464.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.88 Å/pix.
x 96 pix.
= 372.48 Å		3.88 Å/pix.
x 96 pix.
= 372.48 Å		3.88 Å/pix.
x 96 pix.
= 372.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-41.898792 - 50.106679999999997
Average (Standard dev.)-0.021009395 (±3.7999892)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 372.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55464_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55464_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cell lamellae of chlL-deleted C.reinhardtii

EntireName: Cell lamellae of chlL-deleted C.reinhardtii
Components
  • Cell: Cell lamellae of chlL-deleted C.reinhardtii

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Supramolecule #1: Cell lamellae of chlL-deleted C.reinhardtii

SupramoleculeName: Cell lamellae of chlL-deleted C.reinhardtii / type: cell / ID: 1 / Parent: 0
Details: The cell lamellae were generated by cryo-focused ion beam milling.
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 / Chamber humidity: 70 %

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / 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: 5.0 µm / Nominal defocus min: 3.0 µm
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: 24.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 2026
ExtractionNumber tomograms: 32 / Number images used: 12800 / Software - Name: emClarity (ver. 1.5.0.2)
CTF correctionSoftware - Name: emClarity (ver. 1.5.3.10) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 5 / Avg.num./class: 2560 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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