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- EMDB-52579: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated... -

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Basic information

Entry
Database: EMDB / ID: EMD-52579
TitleForm II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
Map datasharpened full map
Sample
  • Complex: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Keywordsribulose-1 / 5-bisphosphate carboxylase/oxygenase / Rubisco / LYASE
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
Ribulose bisphosphate carboxylase
Similarity search - Component
Biological speciesRhodospirillum rubrum ATCC 11170 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsKueffner AM / Zarzycki J / Prinz S / Erb TJ
Funding supportEuropean Union, Germany, 3 items
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, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52579.png

Downloads & links

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Map

FileDownload / File: emd_52579.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.66 Å/pix.
x 360 pix.
= 235.8 Å		0.66 Å/pix.
x 360 pix.
= 235.8 Å		0.66 Å/pix.
x 360 pix.
= 235.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.655 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-47.228523000000003 - 85.023049999999998
Average (Standard dev.)0.000000000001015 (±1.699944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 235.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map B

Fileemd_52579_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_52579_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Form II Rubisco inside EPYC1-formed liquid-liquid phase separated...

EntireName: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
Components
  • Complex: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
    • Protein or peptide: Ribulose bisphosphate carboxylase
  • Ligand: MAGNESIUM ION
  • Ligand: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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Supramolecule #1: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated...

SupramoleculeName: Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Ribulose bisphosphate carboxylase

MacromoleculeName: Ribulose bisphosphate carboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Rhodospirillum rubrum ATCC 11170 (bacteria)
Molecular weightTheoretical: 50.581922 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDQSSRYVNL ALKEEDLIAG GEHVLCAYIM KPKAGYGYVA TAAHFAAESS TGTNVEVCTT DDFTRGVDAL VYEVDEAREL TKIAYPVAL FDRNITDGKA MIASFLTLTM GNNQGMGDVE YAKMHDFYVP EAYRALFDGP SVNISALWKV LGRPEVDGGL V VGTIIKPK ...String:
MDQSSRYVNL ALKEEDLIAG GEHVLCAYIM KPKAGYGYVA TAAHFAAESS TGTNVEVCTT DDFTRGVDAL VYEVDEAREL TKIAYPVAL FDRNITDGKA MIASFLTLTM GNNQGMGDVE YAKMHDFYVP EAYRALFDGP SVNISALWKV LGRPEVDGGL V VGTIIKPK LGLRPKPFAE ACHAFWLGGD FI(KCX)NDEPQGN QPFAPLRDTI ALVADAMRRA QDETGEAKLF SANITADD P FEIIARGEYV LETFGENASH VALLVDGYVA GAAAITTARR RFPDNFLHYH RAGHGAVTSP QSKRGYTAFV HCKMARLQG ASGIHTGTMG FGKMEGESSD RAIAYMLTQD EAQGPFYRQS WGGMKACTPI ISGGMNALRM PGFFENLGNA NVILTAGGGA FGHIDGPVA GARSLRQAWQ AWRDGVPVLD YAREHKELAR AFESFPGDAD QIYPGWRKAL GVEDTRSALP A

UniProtKB: Ribulose bisphosphate carboxylase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

MacromoleculeName: 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: CAP
Molecular weightTheoretical: 356.115 Da
Chemical component information

ChemComp-CAP:
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: sample was blotted for 3 s with blot force 20.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 183006
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC

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