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- EMDB-48648: Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 2... -

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Basic information

Entry
Database: EMDB / ID: EMD-48648
TitleCryo-EM structure of Rubisco from Arabidopsis thaliana with the 2B small subunit isoform
Map data
Sample
  • Complex: Rubisco assembled hexadecamer
    • Complex: Rubisco large subunit
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Complex: Rubisco small subunit 2B
      • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
Keywordscarboxylase / oxygenase / TIM barrel / PHOTOSYNTHESIS
Function / homology
Function and homology information


plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid / reductive pentose-phosphate cycle / response to abscisic acid / chloroplast envelope / chloroplast stroma ...plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid / reductive pentose-phosphate cycle / response to abscisic acid / chloroplast envelope / chloroplast stroma / plastid / chloroplast thylakoid membrane / response to cadmium ion / cytosolic ribosome / chloroplast / monooxygenase activity / protein domain specific binding / mRNA binding / magnesium ion binding
Similarity search - Function
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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-1,5-bisphosphate carboxylase small subunit, N-terminal / Ribulose-1,5-bisphosphate carboxylase small subunit / 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 large chain / Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsCeminsky M / Askey B / Gunn LH
Funding support Sweden, United States, 3 items
OrganizationGrant numberCountry
Carl Trygger Foundation Sweden
National Science Foundation (NSF, United States)DGE-2139899 United States
Department of Energy (DOE, United States)DE-SC0024175 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Rubisco kinetic acclimation at the holoenzyme level.
Authors: Bryce Askey / Maddie Ceminsky / Elena Scott / Yongsheng Wang / Zhen Guo Oh / Stavros Azinas / Arthur Laganowsky / Laura Helen Gunn /
Abstract: In plants, the CO-fixing enzyme Rubisco is hexadecameric, with each mature holoenzyme containing eight small subunits (SSus). Many plants express multiple SSus and vary their expression in response ...In plants, the CO-fixing enzyme Rubisco is hexadecameric, with each mature holoenzyme containing eight small subunits (SSus). Many plants express multiple SSus and vary their expression in response to environmental cues. Previous work indicates that this may allow fine-tuning of Rubisco's performance in a variable environment (i.e., kinetic acclimation). Despite SSu pools being heterogeneous and dynamic, nearly no evidence exists for holoenzyme-level heterogeneity. Here, we characterized the structural and kinetic plasticity of Rubisco. We first established that SSu-heterogeneous Rubisco exists in and quantified the prevalence of heterogeneity. We found SSu-heterogeneous Rubisco to make up over half of the Rubisco pool when heterologously expressed. This Rubisco contained at least four unique SSu ratios, indicating a variety of holoenzyme arrangements are possible. We then tested the kinetic effect of different SSus and found heterogeneity to have an antagonistic effect on substrate and inhibitor affinity. Kinetic differences between the SSus correlated with changes in local flexibility, and cryo-EM analysis illustrated a structural mechanism through which SSus may influence catalysis. Our kinetic and structural findings align with the hypothesized role of SSus in kinetic acclimation, as we observed the warm temperature-expressed SSu of to confer a stabilizing effect to the active site relative to the cool temperature-expressed SSu. This increase in stability manifested as a reduction in flexibility and increase in substrate affinity, indicating that fine-tuning of local stability may underlie Rubisco kinetic acclimation.
History
DepositionJan 14, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48648.png

Downloads & links

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Map

FileDownload / File: emd_48648.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.327
Minimum - Maximum-1.7553387 - 3.0496702
Average (Standard dev.)-0.0014893583 (±0.1163667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48648_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48648_half_map_2.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 : Rubisco assembled hexadecamer

EntireName: Rubisco assembled hexadecamer
Components
  • Complex: Rubisco assembled hexadecamer
    • Complex: Rubisco large subunit
      • Protein or peptide: Ribulose bisphosphate carboxylase large chain
    • Complex: Rubisco small subunit 2B
      • Protein or peptide: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic

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Supramolecule #1: Rubisco assembled hexadecamer

SupramoleculeName: Rubisco assembled hexadecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 12 KDa

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Supramolecule #2: Rubisco large subunit

SupramoleculeName: Rubisco large subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Supramolecule #3: Rubisco small subunit 2B

SupramoleculeName: Rubisco small subunit 2B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 53.020883 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSPQTETKAS VGFKAGVKEY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEP VPGEETQFIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LAALRLEDLR IPPAYTKTFQ GPPHGIQVER D KLNKYGRP ...String:
MSPQTETKAS VGFKAGVKEY KLTYYTPEYE TKDTDILAAF RVTPQPGVPP EEAGAAVAAE SSTGTWTTVW TDGLTSLDRY KGRCYHIEP VPGEETQFIA YVAYPLDLFE EGSVTNMFTS IVGNVFGFKA LAALRLEDLR IPPAYTKTFQ GPPHGIQVER D KLNKYGRP LLGCTIKPKL GLSAKNYGRA VYECLRGGLD FTKDDENVNS QPFMRWRDRF LFCAEAIYKS QAETGEIKGH YL NATAGTC EEMIKRAVFA RELGVPIVMH DYLTGGFTAN TSLSHYCRDN GLLLHIHRAM HAVIDRQKNH GMHFRVLAKA LRL SGGDHI HAGTVVGKLE GDRESTLGFV DLLRDDYVEK DRSRGIFFTQ DWVSLPGVLP VASGGIHVWH MPALTEIFGD DSVL QFGGG TLGHPWGNAP GAVANRVALE ACVQARNEGR DLAVEGNEII REACKWSPEL AAACEVWKEI TFNFPTIDKL DGQE

UniProtKB: Ribulose bisphosphate carboxylase large chain

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

MacromoleculeName: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 15.64389 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MKVWPPIGKK KFETLSYLPD LSDVELAKEV DYLLRNKWIP CVEFELEHGF VYREHGNTPG YYDGRYWTMW KLPLFGCTDS AQVLKEVEE CKKEYPGAFI RIIGFDNTRQ VQCISFIAYK PPSFTEAHHH HHH

UniProtKB: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic

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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

Concentration0.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMC4H13Cl2NO3Tris HCl
50.0 mMNaClsodium chloride
GridMaterial: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 79000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1861242
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Hexadecameric Rubisco from previously solved pdb 5IU0 from an associated deposition
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3.1) / Number images used: 249734
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: Hexadecameric Rubisco from previously solved PDB 5IU0 from associated deposition
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9mur:
Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 2B small subunit isoform

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