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- PDB-9n37: Cryo-EM structure of Rubisco from Arabidopsis thaliana with the 1... -

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Basic information

Entry
Database: PDB / ID: 9n37
TitleCryo-EM structure of Rubisco from Arabidopsis thaliana with the 1A small subunit isoform
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
KeywordsPHOTOSYNTHESIS / carboxylase / oxygenase / TIM barrel
Function / homology
Function and homology information


thylakoid lumen / salicylic acid binding / ribulose bisphosphate carboxylase complex assembly / chloroplast membrane / plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / apoplast / thylakoid / ribulose-bisphosphate carboxylase activity ...thylakoid lumen / salicylic acid binding / ribulose bisphosphate carboxylase complex assembly / chloroplast membrane / plant-type cell wall / photorespiration / ribulose-bisphosphate carboxylase / apoplast / thylakoid / ribulose-bisphosphate carboxylase activity / response to abscisic acid / reductive pentose-phosphate cycle / chloroplast envelope / chloroplast stroma / plastid / chloroplast thylakoid membrane / response to cadmium ion / photosynthesis / cytosolic ribosome / response to cold / chloroplast / monooxygenase activity / copper ion binding / mRNA binding / magnesium ion binding / mitochondrion
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 1A, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsStavros, A. / Askey, B. / Ceminsky, M. / Gunn, L.H.
Funding support Sweden, United States, 2items
OrganizationGrant numberCountry
Carl Trygger Foundation Sweden
National Science Foundation (NSF, United States)DGE-2139899 United States
CitationJournal: To Be Published
Title: Rubisco kinetic acclimation at the holoenzyme level
Authors: Askey, B. / Ceminsky, M. / Scott, E. / Azinas, S. / Guo, Z.G. / Laganowsky, A. / Gunn, L.H.
History
DepositionJan 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 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
I: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
J: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
K: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
L: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
M: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
N: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
O: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
P: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)549,06324
Polymers548,86916
Non-polymers1948
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

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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: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic / RuBisCO small subunit 1A


Mass: 15544.694 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RBCS-1A, ATS1A, At1g67090, F1O19.14, F5A8.1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10795
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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-IDSource
1Rubisco assembled hexadecamerCOMPLEX#1-#20RECOMBINANT
2Rubisco large subunitCOMPLEX#11RECOMBINANT
3Rubisco small subunitCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.55 MDaYES
210.055 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
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)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 491616
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256188 / 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: 83.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003634848
ELECTRON MICROSCOPYf_angle_d0.552347232
ELECTRON MICROSCOPYf_chiral_restr0.04265032
ELECTRON MICROSCOPYf_plane_restr0.0056168
ELECTRON MICROSCOPYf_dihedral_angle_d6.26854820

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