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 minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins

Kueffner, A.M., Pommerkenke, B., Kley, L., Ng, J.Z.Y., Prinz, S., Tinzl-Zechner, M., Claus, P., Paczia, N., Zarzycki, J., Hochberg, G.K.A., Erb, T.J.

To be published.

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