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- EMDB-56142: Subtomogram average of the Chlamydomonas reinhardtii chlororiboso... -

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Basic information

Entry
Database: EMDB / ID: EMD-56142
TitleSubtomogram average of the Chlamydomonas reinhardtii chlororibosome - SSU extension focused
Map data
Sample
  • Complex: Chloroplast ribosome
Keywordschloroplast / ribosome / translation / chlororibosome
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 8.48 Å
AuthorsWaltz F / Engel BD
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation216094 Switzerland
Swiss State Secretariat for Education, Research and InnovationM822.00045 Switzerland
CitationJournal: Biorxiv / Year: 2026
Title: Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome
Authors: Waltz F / Lehner PA / Van der Stappen P / Kater L / Pfeffer S / Engel BD
History
DepositionDec 21, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56142.png

Downloads & links

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Map

FileDownload / File: emd_56142.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.91 Å/pix.
x 320 pix.
= 611.2 Å		1.91 Å/pix.
x 320 pix.
= 611.2 Å		1.91 Å/pix.
x 320 pix.
= 611.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00889
Minimum - Maximum-0.012310138 - 0.031543612
Average (Standard dev.)0.000017188077 (±0.0004713782)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 611.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56142_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56142_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_56142_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 : Chloroplast ribosome

EntireName: Chloroplast ribosome
Components
  • Complex: Chloroplast ribosome

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Supramolecule #1: Chloroplast ribosome

SupramoleculeName: Chloroplast ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: mat3-4

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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: 6.5
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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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: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number subtomograms used: 13245
ExtractionNumber tomograms: 129 / Number images used: 20883 / Method: Template matching / Software - Name: PyTom (ver. pytom-match-pick)
CTF correctionSoftware: (Name: AreTomo (ver. 3), RELION (ver. 5)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
FSC plot (resolution estimation)

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