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- EMDB-56344: Structure of the Chlamydomonas reinhardtii chlororibosome - SSU h... -

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Basic information

Entry
Database: EMDB / ID: EMD-56344
TitleStructure of the Chlamydomonas reinhardtii chlororibosome - SSU head extension recenter and focus
Map data
Sample
  • Complex: Chloroplast ribosome
Keywordschloroplast / ribosome / translation / chlororibosome
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 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
DepositionJan 13, 2026-
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_56344.png

Downloads & links

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Map

FileDownload / File: emd_56344.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 544.307 Å		1.06 Å/pix.
x 512 pix.
= 544.307 Å		1.06 Å/pix.
x 512 pix.
= 544.307 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0631 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0729
Minimum - Maximum-0.97560936 - 1.2702293
Average (Standard dev.)-0.00026977088 (±0.006439569)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 544.3072 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56344_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56344_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_56344_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 : 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / 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
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 225199
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.7)
FSC plot (resolution estimation)

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