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- PDB-9i28: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated... -

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Basic information

Entry
Database: PDB / ID: 9i28
TitleForm II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
ComponentsRibulose bisphosphate carboxylase
KeywordsLYASE / ribulose-1 / 5-bisphosphate carboxylase/oxygenase / Rubisco
Function / homology
Function and homology information


ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase large subunit, type II / Ribulose bisphosphate carboxylase, large chain, active site / Ribulose bisphosphate carboxylase large chain active site. / Ribulose bisphosphate carboxylase, large subunit, ferrodoxin-like N-terminal / Ribulose bisphosphate carboxylase large chain, N-terminal domain / Ribulose bisphosphate carboxylase, large subunit, C-terminal / RuBisCO / Ribulose bisphosphate carboxylase, large subunit, C-terminal domain superfamily / RuBisCO large subunit, N-terminal domain superfamily / Ribulose bisphosphate carboxylase large chain, catalytic domain
Similarity search - Domain/homology
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsKueffner, A.M. / Zarzycki, J. / Prinz, S. / Erb, T.J.
Funding supportEuropean Union, Germany, 3items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 684-2022European Union
Marie Sklodowska-Curie Actions, FragNET ITN101106795 - ECOFixEuropean Union
Max Planck Society Germany
CitationJournal: Nat Plants / Year: 2026
Title: Bottom-up reconstruction of synthetic pyrenoids provides insights into the mechanisms and evolution of carbon concentration by EPYC1 proteins.
Authors: A M Küffner / B Pommerenke / L Kley / J Z Y Ng / S Prinz / M Tinzl-Zechner / L Schulz / P Claus / N Paczia / T Chotel / M Klose / J Zarzycki / G K A Hochberg / T J Erb /
Abstract: Membraneless organelles play essential roles in many cellular processes. In various photosynthetic organisms, they are a crucial part of CO/carbon-concentrating mechanisms (CCMs) that increase ...Membraneless organelles play essential roles in many cellular processes. In various photosynthetic organisms, they are a crucial part of CO/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 fixation via the intrinsically disordered protein essential pyrenoid component 1 (EPYC1). 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.
History
DepositionJan 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase
B: Ribulose bisphosphate carboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,9256
Polymers101,1642
Non-polymers7614
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ribulose bisphosphate carboxylase / RuBisCO


Mass: 50581.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodospirillum rubrum ATCC 11170 (bacteria)
Gene: cbbM, Rru_A2400 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2RRP5, ribulose-bisphosphate carboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.16 MDa / Experimental value: YES
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: sample was blotted for 3 s with blot force 20

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
3EPUimage acquisition
5cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 183006 / Symmetry type: POINT

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