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- EMDB-52438: In-cell Structure of Pyrenoid Rubisco -

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Basic information

Entry
Database: EMDB / ID: EMD-52438
TitleIn-cell Structure of Pyrenoid Rubisco
Map dataSTA Pyrenoid Rubisco in a closed conformation
Sample
  • Complex: Pyrenoid Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit, chloroplastic 1
Keywordschloroplast / pyrenoid / cryo-ET / cryo-FIB / subtomogram averaging / PHOTOSYNTHESIS
Function / homology
Function and homology information


photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / magnesium ion binding
Similarity search - Function
Ribulose bisphosphate carboxylase, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / 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, small subunit / Ribulose bisphosphate carboxylase small subunit, domain / Ribulose bisphosphate carboxylase, small subunit superfamily / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase, small chain / Ribulose bisphosphate carboxylase large subunit, type I / 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 small subunit, chloroplastic 1 / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 8.1 Å
AuthorsNadav E / Zhen H / Maud D / Alireza R / Juan R P / Peijun P
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003339/1 United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: In-cell structure and variability of pyrenoid Rubisco.
Authors: Nadav Elad / Zhen Hou / Maud Dumoux / Alireza Ramezani / Juan R Perilla / Peijun Zhang /
Abstract: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is central to global CO fixation. In eukaryotic algae, its catalytic efficiency is enhanced through the pyrenoid - a protein-dense ...Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is central to global CO fixation. In eukaryotic algae, its catalytic efficiency is enhanced through the pyrenoid - a protein-dense organelle within the chloroplast that concentrates CO. Although Rubisco structure has been extensively studied in vitro, its native structure, dynamics and interactions within the pyrenoid remain elusive. Here, we present the native Rubisco structure inside the green alga Chlamydomonas reinhardtii determined by cryo-electron tomography and subtomogram averaging of cryo-focused ion beam milled cells. Multiple structural subsets of Rubisco are identified, stochastically distributed throughout the pyrenoid. While Rubisco adopts an active conformation in the best-resolved map, comparison among the subsets reveals significant local variations at the active site, at the large subunit dimer interfaces, and at binding protein contact regions. These findings offer a comprehensive understanding of the structure, dynamics, and functional organization of native Rubisco within the pyrenoid, providing valuable insights into its critical role in CO fixation.
History
DepositionDec 30, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52438.png

Downloads & links

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Map

FileDownload / File: emd_52438.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSTA Pyrenoid Rubisco in a closed conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.97 Å/pix.
x 256 pix.
= 504.32 Å		1.97 Å/pix.
x 256 pix.
= 504.32 Å		1.97 Å/pix.
x 256 pix.
= 504.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-14.231144 - 29.887
Average (Standard dev.)-0.000000000034731 (±0.9264237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 504.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52438_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: STA Pyrenoid Rubisco class 12, asymmetric

Fileemd_52438_additional_1.map
AnnotationSTA Pyrenoid Rubisco class 12, asymmetric
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: STA Pyrenoid Rubisco class 13

Fileemd_52438_additional_2.map
AnnotationSTA Pyrenoid Rubisco class 13
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: STA Pyrenoid Rubisco class 10

Fileemd_52438_additional_3.map
AnnotationSTA Pyrenoid Rubisco class 10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: STA Pyrenoid Rubisco class 7

Fileemd_52438_additional_4.map
AnnotationSTA Pyrenoid Rubisco class 7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: STA Pyrenoid Rubisco in a closed conformation, half2 map

Fileemd_52438_half_map_1.map
AnnotationSTA Pyrenoid Rubisco in a closed conformation, half2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: STA Pyrenoid Rubisco in a closed conformation, half1 map

Fileemd_52438_half_map_2.map
AnnotationSTA Pyrenoid Rubisco in a closed conformation, half1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Pyrenoid Rubisco

EntireName: Pyrenoid Rubisco
Components
  • Complex: Pyrenoid Rubisco
    • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Protein or peptide: Ribulose bisphosphate carboxylase small subunit, chloroplastic 1

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Supramolecule #1: Pyrenoid Rubisco

SupramoleculeName: Pyrenoid Rubisco / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-1690

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Macromolecule #1: Ribulose bisphosphate carboxylase large chain

MacromoleculeName: Ribulose bisphosphate carboxylase large chain / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: ribulose-bisphosphate carboxylase
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 51.924039 KDa
SequenceString: TKAGAGFKAG VKDYRLTYYT PDYVVRDTDI LAAFRMTPQL GVPPEECGAA VAAESSTGTW TTVWTDGLTS LDRYKGRCYD IEPVPGEDN QYIAYVAYPI DLFEEGSVTN MFTSIVGNVF GFKALRALRL EDLRIPPAYV KTFVGPPHGI QVERDKLNKY G RGLLGCTI ...String:
TKAGAGFKAG VKDYRLTYYT PDYVVRDTDI LAAFRMTPQL GVPPEECGAA VAAESSTGTW TTVWTDGLTS LDRYKGRCYD IEPVPGEDN QYIAYVAYPI DLFEEGSVTN MFTSIVGNVF GFKALRALRL EDLRIPPAYV KTFVGPPHGI QVERDKLNKY G RGLLGCTI KPKLGLSAKN YGRAVYECLR GGLDFTKDDE NVNSQPFMRW RDRFLFVAEA IYKAQAETGE VKGHYLNATA GT CEEMMKR AVCAKELGVP IIMHDYLTGG FTANTSLAIY CRDNGLLLHI HRAMHAVIDR QRNHGIHFRV LAKALRMSGG DHL HSGTVV GKLEGEREVT LGFVDLMRDD YVEKDRSRGI YFTQDWCSMP GVMPVASGGI HVWHMPALVE IFGDDACLQF GGGT LGHPW GNAPGAAANR VALEACTQAR NEGRDLAREG GDVIRSACKW SPELAAACEV WKEIKFEFDT IDKL

UniProtKB: Ribulose bisphosphate carboxylase large chain

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Macromolecule #2: Ribulose bisphosphate carboxylase small subunit, chloroplastic 1

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit, chloroplastic 1
type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 15.386769 KDa
Recombinant expressionOrganism: Chlamydomonas reinhardtii (plant)
SequenceString:
MMVWTPVNNK MFETFSYLPP LTDEQIAAQV DYIVANGWIP CLEFAEADKA YVSNESAIRF GSVSCLYYDN RYWTMWKLPM FGCRDPMQV LREIVACTKA FPDAYVRLVA FDNQKQVQIM GFLVQRPKTA RDF

UniProtKB: Ribulose bisphosphate carboxylase small subunit, chloroplastic 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.18 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 17713
ExtractionNumber tomograms: 26 / Number images used: 515948
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1gk8

source_name: PDB, initial_model_type: experimental model

1ej7

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9hvm:
In-cell Structure of Pyrenoid Rubisco

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