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- EMDB-18841: Tomogram of T. pseudonana pyrenoid used for subtomogram avergaing -

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Basic information

Entry
Database: EMDB / ID: EMD-18841
TitleTomogram of T. pseudonana pyrenoid used for subtomogram avergaing
Map data
Sample
  • Cell: T. pseudonana
Keywordsmarine diatoms / chloroplast / pyrenoid / photosynthesis / carbon fixation / rubisco
Biological speciesThalassiosira pseudonana (Diatom)
Methodelectron tomography / cryo EM
AuthorsDemulder M / Righetto RD / Wietrzynski W / Lamm L / Engel BD
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)M822.00045European Union
CitationJournal: Cell / Year: 2024
Title: Diatom pyrenoids are encased in a protein shell that enables efficient CO fixation.
Authors: Ginga Shimakawa / Manon Demulder / Serena Flori / Akihiro Kawamoto / Yoshinori Tsuji / Hermanus Nawaly / Atsuko Tanaka / Rei Tohda / Tadayoshi Ota / Hiroaki Matsui / Natsumi Morishima / ...Authors: Ginga Shimakawa / Manon Demulder / Serena Flori / Akihiro Kawamoto / Yoshinori Tsuji / Hermanus Nawaly / Atsuko Tanaka / Rei Tohda / Tadayoshi Ota / Hiroaki Matsui / Natsumi Morishima / Ryosuke Okubo / Wojciech Wietrzynski / Lorenz Lamm / Ricardo D Righetto / Clarisse Uwizeye / Benoit Gallet / Pierre-Henri Jouneau / Christoph Gerle / Genji Kurisu / Giovanni Finazzi / Benjamin D Engel / Yusuke Matsuda /
Abstract: Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO fixation. Diatoms fix up to 20% of global CO, but their pyrenoids remain poorly characterized. ...Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO fixation. Diatoms fix up to 20% of global CO, but their pyrenoids remain poorly characterized. Here, we used in vivo photo-crosslinking to identify pyrenoid shell (PyShell) proteins, which we localized to the pyrenoid periphery of model pennate and centric diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana. In situ cryo-electron tomography revealed that pyrenoids of both diatom species are encased in a lattice-like protein sheath. Single-particle cryo-EM yielded a 2.4-Å-resolution structure of an in vitro TpPyShell1 lattice, which showed how protein subunits interlock. T. pseudonana TpPyShell1/2 knockout mutants had no PyShell sheath, altered pyrenoid morphology, and a high-CO requiring phenotype, with reduced photosynthetic efficiency and impaired growth under standard atmospheric conditions. The structure and function of the diatom PyShell provide a molecular view of how CO is assimilated in the ocean, a critical ecosystem undergoing rapid change.
History
DepositionNov 5, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18841.png

Downloads & links

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Map

FileDownload / File: emd_18841.map.gz / Format: CCP4 / Size: 2.8 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.57 Å/pix.
x 512 pix.
= 4388.864 Å		8.57 Å/pix.
x 1440 pix.
= 12343.68 Å		8.57 Å/pix.
x 1024 pix.
= 8777.728 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.572 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.548639 - 0.58090997
Average (Standard dev.)0.0073405183 (±0.08382601)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-208208-256
Dimensions14401024512
Spacing10241440512
CellA: 8777.728 Å / B: 12343.68 Å / C: 4388.864 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_18841_additional_1.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 : T. pseudonana

EntireName: T. pseudonana (Diatom)
Components
  • Cell: T. pseudonana

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Supramolecule #1: T. pseudonana

SupramoleculeName: T. pseudonana / type: cell / ID: 1 / Parent: 0 / Details: Pyrenoid in T. pseudonana chloroplast
Source (natural)Organism: Thalassiosira pseudonana (Diatom)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos II. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 38

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