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- EMDB-18709: Subtomogram average of the T. pseudonana PyShell -

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Basic information

Entry
Database: EMDB / ID: EMD-18709
TitleSubtomogram average of the T. pseudonana PyShell
Map data
Sample
  • Cell: Thalassiosira pseudonana
Keywordsmarine diatoms / chloroplast / pyrenoid / photosynthesis / carbon fixation / rubisco
Biological speciesThalassiosira pseudonana (Diatom)
Methodsubtomogram averaging / cryo EM / Resolution: 20.0 Å
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
DepositionOct 23, 2023-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18709.png

Downloads & links

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Map

FileDownload / File: emd_18709.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
4.29 Å/pix.
x 64 pix.
= 274.304 Å		4.29 Å/pix.
x 64 pix.
= 274.304 Å		4.29 Å/pix.
x 64 pix.
= 274.304 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.286 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.59271777 - 1.124491
Average (Standard dev.)-0.000000000407277 (±0.14053972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 274.304 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18709_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_18709_half_map_1.map
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Half map: #2

Fileemd_18709_half_map_2.map
Projections & Slices
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Sample components

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Entire : Thalassiosira pseudonana

EntireName: Thalassiosira pseudonana (Diatom)
Components
  • Cell: Thalassiosira pseudonana

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Supramolecule #1: Thalassiosira pseudonana

SupramoleculeName: Thalassiosira pseudonana / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Thalassiosira pseudonana (Diatom)

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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: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.5 sec. / 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 / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
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: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: STOPGAP (ver. 0.7.1) / Number subtomograms used: 14341
ExtractionNumber tomograms: 7 / Number images used: 323629 / Method: Surface sampling / Software - Name: STOPGAP (ver. 0.7.1)
Details: The pyshell surfaces were segmented and oversampled using MemBrain code.
Final angle assignmentType: OTHER / Software - Name: STOPGAP (ver. 0.7.1)
FSC plot (resolution estimation)

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