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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: To Be Published
Title: Bottom-up reconstruction of minimal pyrenoids provides insights into the evolution and mechanisms of carbon concentration by EPYC1 proteins
Authors: Kueffner AM / Pommerkenke B / Kley L / Ng JZY / Prinz S / Tinzl-Zechner M / Claus P / Paczia N / Zarzycki J / Hochberg GKA / Erb TJ
History
DepositionJan 20, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 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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