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- EMDB-51847: 80S Ribosome Average for EMPIAR-11830 -

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Basic information

Entry
Database: EMDB / ID: EMD-51847
Title80S Ribosome Average for EMPIAR-11830
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
KeywordsRibosome
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 4.0 Å
AuthorsKhavnekar S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Mol Cell / Year: 2026
Title: Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii.
Authors: Ron Kelley / Sagar Khavnekar / Ricardo D Righetto / Jessica Heebner / Martin Obr / Xianjun Zhang / Saikat Chakraborty / Grigory Tagiltsev / Alicia K Michael / Sofie van Dorst / Florent Waltz ...Authors: Ron Kelley / Sagar Khavnekar / Ricardo D Righetto / Jessica Heebner / Martin Obr / Xianjun Zhang / Saikat Chakraborty / Grigory Tagiltsev / Alicia K Michael / Sofie van Dorst / Florent Waltz / Caitlyn L McCafferty / Lorenz Lamm / Simon Zufferey / Philippe Van der Stappen / Hugo van den Hoek / Wojciech Wietrzynski / Pavol Harar / William Wan / John A G Briggs / Jürgen M Plitzko / Benjamin D Engel / Abhay Kotecha /
Abstract: In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient ...In situ cryo-electron tomography (cryo-ET) has emerged as the method of choice to investigate the structures of biomolecules in their native context. However, challenges remain for the efficient production and sharing of large-scale cryo-ET datasets. Here, we combined cryogenic plasma-based focused ion beam (cryo-PFIB) milling with recent advances in cryo-ET acquisition and processing to generate a dataset of 1,829 annotated tomograms of the green alga Chlamydomonas reinhardtii, which we provide as a community resource to drive method development and inspire biological discovery. To assay data quality, we performed subtomogram averaging of both soluble and membrane-bound complexes ranging in size from >3 MDa to ∼200 kDa, including 80S ribosomes, Rubisco, nucleosomes, microtubules, clathrin, photosystem II, and mitochondrial ATP synthase. The majority of these density maps reached sub-nanometer resolution, demonstrating the potential of this C. reinhardtii dataset as well as the promise of modern cryo-ET workflows and open data sharing to empower visual proteomics.
History
DepositionOct 18, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51847.png

Downloads & links

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Map

FileDownload / File: emd_51847.map.gz / Format: CCP4 / Size: 132.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 326 pix.
= 638.96 Å		1.96 Å/pix.
x 326 pix.
= 638.96 Å		1.96 Å/pix.
x 326 pix.
= 638.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.009703153 - 0.016607154
Average (Standard dev.)0.000029475428 (±0.0004049458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions326326326
Spacing326326326
CellA=B=C: 638.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_51847_additional_1.map
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Half map: #2

Fileemd_51847_half_map_1.map
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Half map: #1

Fileemd_51847_half_map_2.map
Projections & Slices
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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
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
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
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) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Warp (ver. 2) / Software - details: warptools mcore / Number subtomograms used: 140000
ExtractionNumber tomograms: 14 / Number images used: 200000 / Method: STOPGAP / Software - Name: STOPGAP (ver. 0.7.1)
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4.1.14)Ran through TILTCTF module of TOMOMAN
NOVACTF

Details: Tilt series CTF estimation was done using the TILTCTF program from TOMOMAN v0.9.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationNumber classes: 1 / Software - Name: STOPGAP (ver. 0.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)

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