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- EMDB-54837: Chlamydomonas nuclear envelope-bound ribosome -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54837
TitleChlamydomonas nuclear envelope-bound ribosome
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
Keywordschlamydomonas / nuclear envelope / membrane / ribosome
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 22.7 Å
AuthorsWaltz F / Lamm L / Righetto RD / Engel BD
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss State Secretariat for Education, Research and InnovationM822.00045 Switzerland
CitationJournal: Biorxiv / Year: 2025
Title: MemBrain v2: an end-to-end tool for the analysis of membranes in cryo-electron tomography
Authors: Lamm L / Zufferey S / Zhang H / Righetto RD / Waltz F / Wietrzynski W / Yamauchi KA / Burt A / Liu Y / Martinez-Sanchez A / Ziegler S / Isensee F / Schnabel JA / Engel BD / Peng T
History
DepositionAug 20, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54837.png

Downloads & links

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Map

FileDownload / File: emd_54837.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.64 Å/pix.
x 80 pix.
= 611.2 Å		7.64 Å/pix.
x 80 pix.
= 611.2 Å		7.64 Å/pix.
x 80 pix.
= 611.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-1.7705264 - 4.6200953
Average (Standard dev.)0.000000000173734 (±0.8846388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 611.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54837_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54837_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54837_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 : Chlamydomonas reinhardtii

EntireName: Chlamydomonas reinhardtii (plant)
Components
  • Cell: Chlamydomonas reinhardtii

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Supramolecule #1: Chlamydomonas reinhardtii

SupramoleculeName: Chlamydomonas reinhardtii / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-3994 mat3-4 mt+

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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 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE-PROPANE / 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) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 22.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.7.1) / Number subtomograms used: 4515
ExtractionNumber tomograms: 92 / Number images used: 4515 / Software - Name: STOPGAP (ver. 0.7.4)
Software - details: As detailed above, the particles were first selected using the MemBrain-pick package, and subsequently extracted using STOPGAP.
Details: Particles were picked using MemBrain-pick and extracted using STOPGAP.
CTF correctionSoftware:
Namedetails
TOMOMANCTF estimation using TILTCTF module
IMOD

Details: Tilt series CTF estimation was done using the TILTCTF program from TOMOMAN v0.9. CTF-corrected tomograms were calculated using IMOD.
Type: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER / Software - Name: STOPGAP (ver. 0.7.1)
FSC plot (resolution estimation)

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