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- PDB-9o49: Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I -

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Basic information

Entry
Database: PDB / ID: 9o49
TitleCryo-EM structure of Rubisco with hetero small subunit 1A3B form I
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
  • Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
KeywordsPLANT PROTEIN / rubisco / Arabidopsis thaliana / hetero small subunit
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 / ribulose-bisphosphate carboxylase activity / apoplast / thylakoid ...thylakoid lumen / salicylic acid binding / ribulose bisphosphate carboxylase complex assembly / chloroplast membrane / 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 / photosynthesis / cytosolic ribosome / response to cold / chloroplast / monooxygenase activity / copper ion binding / protein domain specific 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 / Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhang, Z. / Bolla, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Rubisco with hetero small subunit 1A3B form I
Authors: Zhang, Z. / Bolla, J.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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 subunit 3B, chloroplastic
J: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
K: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
L: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
M: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
N: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
O: Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic
P: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic


Theoretical massNumber of molelcules
Total (without water)586,48516
Polymers586,48516
Non-polymers00
Water00
1


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

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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 natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: O03042, ribulose-bisphosphate carboxylase
#2: Protein
Ribulose bisphosphate carboxylase small subunit 3B, chloroplastic / RuBisCO small subunit 3B


Mass: 20307.338 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P10798
#3: Protein Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic / RuBisCO small subunit 1A


Mass: 20237.104 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P10795
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

ComponentName: rubisco / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14328 / Symmetry type: POINT
RefinementHighest resolution: 2.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00335842
ELECTRON MICROSCOPYf_angle_d0.4748606
ELECTRON MICROSCOPYf_dihedral_angle_d10.3513054
ELECTRON MICROSCOPYf_chiral_restr0.0415144
ELECTRON MICROSCOPYf_plane_restr0.0046340

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