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- EMDB-55459: In-cell structure of dark-treated chlL-deleted C.reinhardtii chlo... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55459
TitleIn-cell structure of dark-treated chlL-deleted C.reinhardtii chloroplast 70S ribosome in non-translation state
Map data
Sample
  • Cell: Cell lamellae of chlL-deleted C.reinhardtii
KeywordsChloroplast 70S ribosome / 70S ribosome / green algae / Chlamydomonas reinhardtii / RIBOSOME
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 6.4 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_55459.png

Downloads & links

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Map

FileDownload / File: emd_55459.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.94 Å/pix.
x 196 pix.
= 380.24 Å		1.94 Å/pix.
x 196 pix.
= 380.24 Å		1.94 Å/pix.
x 196 pix.
= 380.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.8
Minimum - Maximum-49.48715 - 70.484343999999993
Average (Standard dev.)0.37546664 (±4.0759254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 380.24002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55459_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55459_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_55459_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 : 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: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 9757
ExtractionNumber tomograms: 152 / Number images used: 22800 / 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: 3000 / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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