9I28 | pdb_00009i28

Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP

• PDB DOI: https://doi.org/10.2210/pdb9I28/pdb
• EM Map EMD-52579: EMDB EMDataResource

• Classification: LYASE
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-01-20 Released: 2026-02-04 
• Deposition Author(s): Kueffner, A.M., Zarzycki, J., Prinz, S., Erb, T.J.
• Funding Organization(s): European Molecular Biology Organization (EMBO), Marie Sklodowska-Curie Actions, FragNET ITN, Max Planck Society

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Bottom-up reconstruction of synthetic pyrenoids provides insights into the mechanisms and evolution of carbon concentration by EPYC1 proteins.

Kuffner, A.M., Pommerenke, B., Kley, L., Ng, J.Z.Y., Prinz, S., Tinzl-Zechner, M., Schulz, L., Claus, P., Paczia, N., Chotel, T., Klose, M., Zarzycki, J., Hochberg, G.K.A., Erb, T.J.

(2026) Nat Plants 12: 1622-1636

• PubMed: 42601498 
• DOI: https://doi.org/10.1038/s41477-026-02349-x
• Primary Citation Related Structures: 
  9I26, 9I27, 9I28


• PubMed Abstract: 
  

  Membraneless organelles play essential roles in many cellular processes. In various photosynthetic organisms, they are a crucial part of CO ₂ /carbon-concentrating mechanisms (CCMs) that increase photosynthetic productivity. One example is the pyrenoid in Chlamydomonas reinhardtii, a liquid-phase-separated organelle that localizes and improves CO ₂ fixation via the intrinsically disordered protein essential pyrenoid component 1 (EPYC1 _CR ). Modern-day pyrenoids are complex structures with an elaborate cellular architecture and dozens of components, raising the question of how they could have developed from simpler condensates. Here we develop a bottom-up approach to study the function of EPYC1s and explore their sequence-function space across phylogenetic diversity and evolution. We demonstrate that extant and ancestral EPYC1 sequences induce phase separation of Rubisco into synthetic pyrenoids with functional CCMs. Surprisingly, these CCMs are mainly based on enhanced carboxylation rates (rather than increased specificity), offering new insights into the construction, function and evolution of natural and synthetic pyrenoids.

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Organizational Affiliation: 
• Research Group Sustainable Biocatalysis, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. [e-mail].
Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
Phillips-University of Marburg, Marburg, Germany.
Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt, Germany.
Microbes-for-Climate (SYNMIKRO), Marburg, Germany.
Department of Biochemistry & Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany. [e-mail].
Microbes-for-Climate (SYNMIKRO), Marburg, Germany. [e-mail].
Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 101.92 kDa 
• Atom Count: 6,908 
• Modeled Residue Count: 898 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	A, B	466	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: cbbM, Rru_A2400 EC: 4.1.1.39
UniProt
Find proteins for Q2RRP5 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RRP5  Go to UniProtKB:  Q2RRP5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAP (Subject of Investigation/LOI)	D [auth A], F [auth B]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C6 H14 O13 P2 ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG (Subject of Investigation/LOI)	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A, B	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.93 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Kueffner, A.M., Zarzycki, J., Prinz, S., Erb, T.J.

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Funding Organization	Location	Grant Number
European Molecular Biology Organization (EMBO)	European Union	ALTF 684-2022
Marie Sklodowska-Curie Actions, FragNET ITN	European Union	101106795 - ECOFix
Max Planck Society	Germany	--

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release
  
• Version 1.1: 2026-08-19
  Changes: Data collection, Database references
• Version 1.2: 2026-08-26
  Changes: Data collection, Database references