8WQP

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 CO2 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, D.R., Uwizeye, C., Gallet, B., Jouneau, H.P., Gerle, C., Kurisu, G., Finazzi, G., Engel, D.B., Matsuda, Y.

(2024) Cell 187: 1-16

• DOI: https://doi.org/10.1016/j.cell.2024.09.013

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 
• Modelled 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