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

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Basic information

Entry
Database: PDB / ID: 9pvb
TitleHybrid Rubisco containing Arabidopsis thaliana large subunit and Nicotiana tabacum trichome isoform 2 small subunit
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit, 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 / plasmodesma / response to abscisic acid / chloroplast envelope ...plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid / reductive pentose-phosphate cycle / plasmodesma / 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 small subunit, chloroplastic / Ribulose bisphosphate carboxylase large chain
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
Arabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.04 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: 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

Downloads & links

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Assembly

Deposited unit
A: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase large chain
D: Ribulose bisphosphate carboxylase large chain
B: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase large chain
G: Ribulose bisphosphate carboxylase large chain
H: Ribulose bisphosphate carboxylase large chain
F: Ribulose bisphosphate carboxylase large chain
M: Ribulose bisphosphate carboxylase small subunit, chloroplastic
K: Ribulose bisphosphate carboxylase small subunit, chloroplastic
O: Ribulose bisphosphate carboxylase small subunit, chloroplastic
P: Ribulose bisphosphate carboxylase small subunit, chloroplastic
N: Ribulose bisphosphate carboxylase small subunit, chloroplastic
I: Ribulose bisphosphate carboxylase small subunit, chloroplastic
J: Ribulose bisphosphate carboxylase small subunit, chloroplastic
L: Ribulose bisphosphate carboxylase small subunit, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)523,35432
Polymers520,31016
Non-polymers3,04316
Water30,1211672
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: 50804.406 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: 1a2b3b
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit, chloroplastic / RuBisCO small subunit


Mass: 14234.376 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: LOC107775666, RBCS / Production host: Arabidopsis thaliana (thale cress) / Strain (production host): 1a2b3b Nt-2 / References: UniProt: A0A1S3YFM5
#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.: 1672 / 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 Nicotiana tabacum trichome isoform 2 small subunitCOMPLEX#1-#20RECOMBINANT
2Arabidopsis thaliana Rubisco large subunitCOMPLEX#11RECOMBINANT
3Nicotiana tabacum Rubisco small subunitCOMPLEX#21RECOMBINANTtrichome type small subunit, isoform 2
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.55 MDaYES
220.55 MDaYES
310.014 MDaYES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Nicotiana tabacum (common tobacco)4097
32Arabidopsis thaliana (thale cress)37021a2b3b
43Nicotiana tabacum (common tobacco)4097
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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
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)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
4cryoSPARC3CTF correction
7Cootmodel fitting
12cryoSPARC33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 916243
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 528218 / Num. of class averages: 1 / 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
RefinementHighest resolution: 2.04 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00338701
ELECTRON MICROSCOPYf_angle_d0.61152644
ELECTRON MICROSCOPYf_dihedral_angle_d8.7925445
ELECTRON MICROSCOPYf_chiral_restr0.0465552
ELECTRON MICROSCOPYf_plane_restr0.0056887

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