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- PDB-9pvc: Hybrid Rubisco containing Arabidopsis thaliana large subunit and ... -

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Basic information

Entry
Database: PDB / ID: 9pvc
TitleHybrid Rubisco containing Arabidopsis thaliana large subunit and Chlamydomonas reinhardtii small subunit
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small chain 2, chloroplastic
KeywordsPHOTOSYNTHESIS / carboxylase / oxygenase / TIM barrel / Calvin-Benson-Bassham Cycle
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 / monooxygenase activity / chloroplast / cytosolic ribosome / mRNA binding / 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
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE / Ribulose bisphosphate carboxylase large chain / Ribulose bisphosphate carboxylase small subunit, chloroplastic 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Chlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.08 Å
AuthorsAzinas, S. / Ceminsky, M. / Gunn, L.H.
Funding support Sweden, United States, 2items
OrganizationGrant numberCountry
Carl Trygger Foundation Sweden
Department of Energy (DOE, United States) United States
CitationJournal: To Be Published
Title: Heterologous small subunits complement growth and modify Rubisco catalysis in Arabidopsis
Authors: Mao, Y. / Azinas, S. / Ceminsky, M. / Orr, D. / Gunn, L.H. / McCormick, A.J.
History
DepositionAug 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 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

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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 chain 2, chloroplastic
J: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
K: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
L: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
M: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
N: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
O: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
P: Ribulose bisphosphate carboxylase small chain 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)592,89832
Polymers589,85516
Non-polymers3,04316
Water33,7601874
1


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

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Components

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


Mass: 53063.883 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: Arabidopsis thaliana (thale cress) / Strain (production host): 1a2b3b
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small chain 2, chloroplastic / RuBisCO small subunit 2


Mass: 20667.959 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: RBCS-2 / Production host: Arabidopsis thaliana (thale cress) / Strain (production host): 1a2b3b
References: UniProt: P08475, ribulose-bisphosphate carboxylase
#3: Sugar
ChemComp-CAP / 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE


Type: saccharide / Mass: 356.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O13P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1874 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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-IDSourceDetails (eV)
1Rubisco containing Arabidopsis thaliana large subunit and Chlamydomonas reinhardtii small subunitCOMPLEX#1-#20RECOMBINANT
2Arabidopsis thaliana Rubisco large subunitCOMPLEX#11RECOMBINANT
3Chlamydomonas reinhardtii Rubisco small subunitCOMPLEX#21RECOMBINANTRbcS2
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.55 MDaYES
220.55 MDaYES
310.014 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Chlamydomonas reinhardtii (plant)3055
32Arabidopsis thaliana (thale cress)37021a2b3b
43Chlamydomonas reinhardtii (plant)3055
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Arabidopsis thaliana (thale cress)37021a2b3b
32Arabidopsis thaliana (thale cress)37021a2b3b
33Arabidopsis thaliana (thale cress)37021a2b3b
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 7354

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARC3CTF correction
12cryoSPARC3classification
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2394466
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 593150 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 5IU0

5iu0


Accession code: 5IU0 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00340376
ELECTRON MICROSCOPYf_angle_d0.629755008
ELECTRON MICROSCOPYf_chiral_restr0.04575840
ELECTRON MICROSCOPYf_plane_restr0.00527208
ELECTRON MICROSCOPYf_dihedral_angle_d6.56025699

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