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- PDB-9mur: Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 2... -

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Basic information

Entry
Database: PDB / ID: 9mur
TitleCryo-EM structure of Rubisco from Arabidopsis thaliana with the 2B small subunit isoform
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
KeywordsPHOTOSYNTHESIS / carboxylase / oxygenase / TIM barrel
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsCeminsky, M. / Askey, B. / Gunn, L.H.
Funding support Sweden, United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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 large chain
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
J: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
K: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
L: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
M: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
N: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
O: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic
P: Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic


Theoretical massNumber of molelcules
Total (without water)549,31816
Polymers549,31816
Non-polymers00
Water00
1


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

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Components

#1: Protein
Ribulose bisphosphate carboxylase large chain / RuBisCO large subunit


Mass: 53020.883 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: rbcL, AtCg00490
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit 2B, chloroplastic / RuBisCO small subunit 2B


Mass: 15643.890 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RBCS-2B, ATS2B, At5g38420, MXI10.14
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10797
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

Component
IDNameTypeEntity IDParent-IDSource
1Rubisco assembled hexadecamerCOMPLEXall0RECOMBINANT
2Rubisco large subunitCOMPLEX#11RECOMBINANT
3Rubisco small subunit 2BCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.55 MDaYES
210.056 MDaYES
310.012 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Arabidopsis thaliana (thale cress)3702
32Arabidopsis thaliana (thale cress)3702
43Arabidopsis thaliana (thale cress)3702
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
32Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
43Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)866768
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris HClC4H13Cl2NO31
250 mMsodium chlorideNaCl1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3.1particle selection
2EPUimage acquisition
4cryoSPARC4.3.1CTF correction
7Coot0.9.8.1model fitting
9cryoSPARC4.3.1initial Euler assignment
10cryoSPARC4.3.1final Euler assignment
11cryoSPARC4.3.1classification
12cryoSPARC4.3.13D reconstruction
13PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1861242
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249734 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingDetails: Hexadecameric Rubisco from previously solved PDB 5IU0 from associated deposition
Source name: Other / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.85 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005835834
ELECTRON MICROSCOPYf_angle_d0.732248578
ELECTRON MICROSCOPYf_chiral_restr0.05115137
ELECTRON MICROSCOPYf_plane_restr0.00656333
ELECTRON MICROSCOPYf_dihedral_angle_d6.81064912

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