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- EMDB-37751: Cryo-EM structure of T. pseudonana PyShell helical tube -

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Basic information

Entry
Database: EMDB / ID: EMD-37751
TitleCryo-EM structure of T. pseudonana PyShell helical tube
Map data
Sample
  • Complex: in vitro tube structure of T. pseudonana PyShell
    • Protein or peptide: Diatom the pyrenoid shell protein
Keywordsmarine diatoms / photosynthesis / CO2-concentrating mechanism / pyrenoids / PLANT PROTEIN
Function / homologyUncharacterized protein
Function and homology information
Biological speciesThalassiosira pseudonana (Diatom)
Methodhelical reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsKawamoto A / Tohda R / Gerle C / Kurisu G
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
Japan Society for the Promotion of Science (JSPS)19H01153 Japan
Japan Science and TechnologyJPMJCR20E1 Japan
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 12, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37751.png

Downloads & links

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Map

FileDownload / File: emd_37751.map.gz / Format: CCP4 / Size: 614.1 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.)
1.09 Å/pix.
x 544 pix.
= 591.6 Å		1.09 Å/pix.
x 544 pix.
= 591.6 Å		1.09 Å/pix.
x 544 pix.
= 591.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0875 Å
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Contour LevelBy AUTHOR: 0.0075
Minimum - Maximum-0.070884325 - 0.113890864
Average (Standard dev.)0.000003702391 (±0.00048322315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions544544544
Spacing544544544
CellA=B=C: 591.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37751_msk_1.map
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Additional map: #1

Fileemd_37751_additional_1.map
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Additional map: #2

Fileemd_37751_additional_2.map
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Half map: #1

Fileemd_37751_half_map_1.map
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Half map: #2

Fileemd_37751_half_map_2.map
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Sample components

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Entire : in vitro tube structure of T. pseudonana PyShell

EntireName: in vitro tube structure of T. pseudonana PyShell
Components
  • Complex: in vitro tube structure of T. pseudonana PyShell
    • Protein or peptide: Diatom the pyrenoid shell protein

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Supramolecule #1: in vitro tube structure of T. pseudonana PyShell

SupramoleculeName: in vitro tube structure of T. pseudonana PyShell / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thalassiosira pseudonana (Diatom)

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Macromolecule #1: Diatom the pyrenoid shell protein

MacromoleculeName: Diatom the pyrenoid shell protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thalassiosira pseudonana (Diatom)
Molecular weightTheoretical: 24.98602 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)WDN SSPVIVQGGS LRTWSFANPA IESVQVLLKT EGRPLDADVE LW QGPDNTP HKMRVYVEDG ALRTFNAVIG TPRGPNTVAI RNIGQLEFPL DAVVRPDRDD GLAAGIASVA TRSETIQGGA LRT YPFNPT ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)WDN SSPVIVQGGS LRTWSFANPA IESVQVLLKT EGRPLDADVE LW QGPDNTP HKMRVYVEDG ALRTFNAVIG TPRGPNTVAI RNIGQLEFPL DAVVRPDRDD GLAAGIASVA TRSETIQGGA LRT YPFNPT VDSVAIILKT DGRPLNARIE LLQGPNNNKQ VVELYTEDGL DRPFFAIVET PGSGNVVRVV NTAPVEFPLY ASVD AYRVG GGGDWADDGL MIGRAF

UniProtKB: Uncharacterized protein

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
0.3 MNaClsodium chloride
50.0 mMTris-HClTris Hydrochloride Acid
1.0 mMEDTAethylenediaminetetraacetic acid
1.0 mMDTTdithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5951 / Average exposure time: 2.631 sec. / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie-mode at 52 frames per second
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
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 - Helical parameters - Δz: 3.59 Å
Applied symmetry - Helical parameters - Δ&Phi: -56.07 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 322887
Segment selectionNumber selected: 5951 / Software - Name: RELION (ver. 3.1)
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8wqp:
Cryo-EM structure of T. pseudonana PyShell helical tube

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