8WQP | pdb_00008wqp

Cryo-EM structure of T. pseudonana PyShell helical tube

• PDB DOI: https://doi.org/10.2210/pdb8WQP/pdb
• EM Map EMD-37751: EMDB EMDataResource

• Classification: PLANT PROTEIN
• Organism(s): Thalassiosira pseudonana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-10-12 Released: 2024-10-09 
• Deposition Author(s): Kawamoto, A., Tohda, R., Gerle, C., Kurisu, G.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Starting Model: in silico

Literature

Diatom pyrenoids are encased in a protein shell that enables efficient CO 2 fixation.

Shimakawa, G., Demulder, M., Flori, S., Kawamoto, A., Tsuji, Y., Nawaly, H., Tanaka, A., Tohda, R., Ota, T., Matsui, H., Morishima, N., Okubo, R., Wietrzynski, W., Lamm, L., Righetto, R.D., Uwizeye, C., Gallet, B., Jouneau, P.H., Gerle, C., Kurisu, G., Finazzi, G., Engel, B.D., Matsuda, Y.

(2024) Cell 187: 5919

• PubMed: 39357521 
• DOI: https://doi.org/10.1016/j.cell.2024.09.013
• Primary Citation of Related Structures:  
  8WQP


• PubMed Abstract: 
  

  Pyrenoids are subcompartments of algal chloroplasts that increase the efficiency of Rubisco-driven CO ₂ fixation. Diatoms fix up to 20% of global CO ₂ , 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 ₂ 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 ₂ is assimilated in the ocean, a critical ecosystem undergoing rapid change.

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Organizational Affiliation: 
• Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan.
Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara 903-0213, Japan.
Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland; HelmholtzAI, Helmholtz Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble-Alpes, CNRS, CEA, INRAE, IRIG-DBSCI, 17 rue des Martyrs, 38000 Grenoble, France.
University of Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France.
University of Grenoble Alpes, CEA, IRIG-MEM, 38000 Grenoble, France.
Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland. Electronic address: [e-mail].
Department of Bioscience, School of Biological and Environmental Sciences, Kwansei Gakuin University, 1 Gakuen-Uegahara, Sanda, Hyogo 669-1330, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.97 kDa 
• Atom Count: 3,512 
• Modeled Residue Count: 466 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diatom the pyrenoid shell protein	A, B	233	Thalassiosira pseudonana	Mutation(s): 0  Gene Names: THAPSDRAFT_7881
UniProt
Find proteins for B8C7S8 (Thalassiosira pseudonana) Explore B8C7S8  Go to UniProtKB:  B8C7S8

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.40 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Kawamoto, A., Tohda, R., Gerle, C., Kurisu, G.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23H04958
Japan Society for the Promotion of Science (JSPS)	Japan	19H01153
Japan Science and Technology	Japan	JPMJCR20E1

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references