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- EMDB-59304: EM map of in-cell structure of the arch-moved chloroplast ribosom... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-59304
TitleEM map of in-cell structure of the arch-moved chloroplast ribosome in Chlamydomonas reinhardtii
Map data
Sample
  • Cell: Wild-type Chlamydomonas reinhardtii cell
Keywordsin-cell / chloroplast / ribosome / Chlamydomonas reinhardtii
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 8.4 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: In-cell structural analysis reveals a distinctive chloroplast ribosome in Chlamydomonas reinhardtii
Authors: Hou Z / Shen Y / Zhang Z / Lu P / Katzourakis A / Zhang P
History
DepositionAug 4, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59304.png

Downloads & links

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Map

FileDownload / File: emd_59304.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 256 pix.
= 487.168 Å		1.9 Å/pix.
x 256 pix.
= 487.168 Å		1.9 Å/pix.
x 256 pix.
= 487.168 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.903 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0898
Minimum - Maximum-0.1995069 - 0.51238364
Average (Standard dev.)0.004940734 (±0.02983674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 487.168 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_59304_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_59304_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_59304_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 : Wild-type Chlamydomonas reinhardtii cell

EntireName: Wild-type Chlamydomonas reinhardtii cell
Components
  • Cell: Wild-type Chlamydomonas reinhardtii cell

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Supramolecule #1: Wild-type Chlamydomonas reinhardtii cell

SupramoleculeName: Wild-type Chlamydomonas reinhardtii cell / 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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 298.15 K / Instrument: OTHER
Details: The value given for _em_vitrification.instrument is LEICA EM GP2. This is not in a list of allowed values {'SPT LABTECH CHAMELEON', 'FEI VITROBOT MARK II', 'LEICA KF80', 'EMS-002 RAPID ...Details: The value given for _em_vitrification.instrument is LEICA EM GP2. This is not in a list of allowed values {'SPT LABTECH CHAMELEON', 'FEI VITROBOT MARK II', 'LEICA KF80', 'EMS-002 RAPID IMMERSION FREEZER', 'LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'ZEISS PLUNGE FREEZER CRYOBOX', 'FEI VITROBOT MARK IV', 'CRYOSOL VITROJET', 'FEI VITROBOT MARK III', 'FEI VITROBOT MARK I', 'HOMEMADE PLUNGER', 'LEICA PLUNGER', 'LEICA EM GP', 'REICHERT-JUNG PLUNGER', 'SPOTITON', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 2430
ExtractionNumber tomograms: 260 / Number images used: 49911 / 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: 10 / Avg.num./class: 4991 / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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