9HVM | pdb_00009hvm

In-cell Structure of Pyrenoid Rubisco

• PDB DOI: https://doi.org/10.2210/pdb9HVM/pdb
• EM Map EMD-52438: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Chlamydomonas reinhardtii
• Expression System: Chlamydomonas reinhardtii
• Mutation(s): No 


• Deposited: 2024-12-30 Released: 2025-03-05 
• Deposition Author(s): Nadav, E., Zhen, H., Maud, D., Alireza, R., Juan R, P., Peijun, P.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 8.10 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

Starting Models: experimental

Literature

In-cell structure and variability of pyrenoid Rubisco.

Elad, N., Hou, Z., Dumoux, M., Ramezani, A., Perilla, J.R., Zhang, P.

(2025) Nat Commun 16: 7763-7763

• PubMed: 40835820 
• DOI: https://doi.org/10.1038/s41467-025-62998-y
• Primary Citation of Related Structures:  
  9HVM


• PubMed Abstract: 
  

  Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is central to global CO ₂ fixation. In eukaryotic algae, its catalytic efficiency is enhanced through the pyrenoid - a protein-dense organelle within the chloroplast that concentrates CO ₂ . Although Rubisco structure has been extensively studied in vitro, its native structure, dynamics and interactions within the pyrenoid remain elusive. Here, we present the native Rubisco structure inside the green alga Chlamydomonas reinhardtii determined by cryo-electron tomography and subtomogram averaging of cryo-focused ion beam milled cells. Multiple structural subsets of Rubisco are identified, stochastically distributed throughout the pyrenoid. While Rubisco adopts an active conformation in the best-resolved map, comparison among the subsets reveals significant local variations at the active site, at the large subunit dimer interfaces, and at binding protein contact regions. These findings offer a comprehensive understanding of the structure, dynamics, and functional organization of native Rubisco within the pyrenoid, providing valuable insights into its critical role in CO ₂ fixation.

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Organizational Affiliation: 
• Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
The Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK.
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK. [e-mail].
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Oxford, UK. [e-mail].
Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Hetero 16-mer - A8B8 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 538.49 kDa 
• Atom Count: 37,816 
• Modeled Residue Count: 4,808 
• Deposited Residue Count: 4,808 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase large chain	A, C, E, G, I, K, M, O	469	Chlamydomonas reinhardtii	Mutation(s): 0  EC: 4.1.1.39
UniProt
Find proteins for P00877 (Chlamydomonas reinhardtii) Explore P00877  Go to UniProtKB:  P00877

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase small subunit, chloroplastic 1	B, D, F, H, J, L, N, P	132	Chlamydomonas reinhardtii	Mutation(s): 0  Gene Names: RBCS1, RBCS-1, CHLRE_02g120100v5, CHLREDRAFT_82986
UniProt
Find proteins for P00873 (Chlamydomonas reinhardtii) Explore P00873  Go to UniProtKB:  P00873

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 8.10 Å
• Aggregation State: CELL 
• Reconstruction Method: SUBTOMOGRAM AVERAGING 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Nadav, E., Zhen, H., Maud, D., Alireza, R., Juan R, P., Peijun, P.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/S003339/1

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release
  
• Version 1.1: 2025-09-17
  Changes: Data collection, Database references