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- EMDB-51731: In situ PSII subtomogram average from Chlamydomonas reinhardtii -

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Basic information

Entry
Database: EMDB / ID: EMD-51731
TitleIn situ PSII subtomogram average from Chlamydomonas reinhardtii
Map data
Sample
  • Cell: Chlamydomonas reinhardtii
Keywordscryo-et / chlamydomonas / tomography / in situ / membrane / PHOTOSYNTHESIS
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 18.8 Å
Authorsvan Dorst S / Heebner JE / Lamm L / Righetto RD / Wietrzynski W / Khavnekar S / Kotecha A / Engel BD
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss State Secretariat for Education, Research and InnovationM822.00045 Switzerland
Citation
Journal: 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.
#1: Journal: Biorxiv / Year: 2024
Title: Towards community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii
Authors: Kelley R / Khavnekar S / Righetto RD / Heebner J / Obr M / Zhang X / Chakraborty S / Tagiltsev G / Michael AK / van Dorst S / Waltz F / McCafferty CL / Lamm L / Zufferey S / Van der Stappen ...Authors: Kelley R / Khavnekar S / Righetto RD / Heebner J / Obr M / Zhang X / Chakraborty S / Tagiltsev G / Michael AK / van Dorst S / Waltz F / McCafferty CL / Lamm L / Zufferey S / Van der Stappen P / van den Hoek H / Wietrzynski W / Harar P / Wan W / Briggs JA / Plitzko JM / Engel BD / Kotecha A
History
DepositionOct 4, 2024-
Header (metadata) releaseNov 6, 2024-
Map releaseNov 6, 2024-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51731.png

Downloads & links

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Map

FileDownload / File: emd_51731.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.96 Å/pix.
x 240 pix.
= 470.4 Å		1.96 Å/pix.
x 240 pix.
= 470.4 Å		1.96 Å/pix.
x 240 pix.
= 470.4 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: 0.02
Minimum - Maximum-0.12951437 - 0.1648417
Average (Standard dev.)-0.000000000000001 (±0.019341636)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 470.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51731_msk_1.map
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Half map: #2

Fileemd_51731_half_map_1.map
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Half map: #1

Fileemd_51731_half_map_2.map
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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
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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 18.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 3123
ExtractionNumber tomograms: 21 / Number images used: 22917 / Method: AI voxel-based segmentation / Software - Name: STOPGAP (ver. 0.7.1) / Details: Initial angles assigned with MemBrain.
CTF correctionSoftware:
Namedetails
CTFFIND (ver. 4.1.14)Ran through TILTCTF module of TOMOMAN
RELION (ver. 4.0.1)

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: 4 / Software - Name: STOPGAP (ver. 0.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1)

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