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- PDB-9l5i: CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 sy... -

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Basic information

Entry
Database: PDB / ID: 9l5i
TitleCryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Components
  • Ribulose bisphosphate carboxylase large chain
  • Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
KeywordsPHOTOSYNTHESIS / CO2 fixation
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 / 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: 1.74 Å
AuthorsYamori, W. / Nakazato, I. / Yuchen, Q. / Sanga, Y. / Miyata, T. / Uehara, R. / Noto, Y. / Namba, K. / Fukayama, H. / Matsumura, H. / Arimura, S.
Funding support Japan, 8items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24H02277 Japan
Japan Society for the Promotion of Science (JSPS)24K01994 Japan
Japan Society for the Promotion of Science (JSPS)23K18033 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101117 Japan
Japan Agency for Medical Research and Development (AMED)JP22ama121003 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121001 Japan
Japan Agency for Medical Research and Development (AMED)JP17pc0101020 Japan
Japan Science and TechnologyJPMJOP1861 Japan
CitationJournal: To Be Published
Title: CryoEM structure of Arabidopsis thaliana D397N Rubisco with D4 symmetry
Authors: Yamori, W. / Nakazato, I. / Yuchen, Q. / Sanga, Y. / Miyata, T. / Uehara, R. / Noto, Y. / Namba, K. / Fukayama, H. / Matsumura, H. / Arimura, S.
History
DepositionDec 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2026Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 20, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 20, 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
S: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
B: Ribulose bisphosphate carboxylase large chain
C: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
D: Ribulose bisphosphate carboxylase large chain
E: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
F: Ribulose bisphosphate carboxylase large chain
G: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
H: Ribulose bisphosphate carboxylase large chain
I: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
J: Ribulose bisphosphate carboxylase large chain
K: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
L: Ribulose bisphosphate carboxylase large chain
M: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
N: Ribulose bisphosphate carboxylase large chain
O: Ribulose bisphosphate carboxylase small subunit 1A, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)586,82524
Polymers586,05616
Non-polymers7698
Water41,8672324
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: 53019.898 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 1A, chloroplastic / RuBisCO small subunit 1A


Mass: 20237.104 Da / Num. of mol.: 8 / Source method: isolated from a natural source
Details: The amino acid sequences of RBCS2B and RBCS3B, which cause microheterogeneity, are registered in GenBank under accession numbers AAO29974.1 and AAL47390.1.
Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P10795
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2324 / 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

ComponentName: Rubisco / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 8
Details: 80 mM HEPES-KOH pH 8.0, 5 mM DTT, 1 mM EDTA, 50 mM ammonium sulfate
Buffer componentConc.: 50 mM / Name: ammonium sulfate / Formula: (NH4)2SO4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2732
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2SerialEM3.9image acquisition
4CTFFINDCTF correction
7UCSF Chimera1.16model fitting
8Coot0.9.6model fitting
10PHENIX1.20.1_4487model refinement
11RELION4initial Euler assignment
12RELION4final Euler assignment
14RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2302408
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 1.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 904485 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Accession code: 6KYI / Initial refinement model-ID: 1 / PDB-ID: 6KYI

6kyi

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-IDChain residue rangePdb chain residue range
1AA21-46421-464
2BB20-46220-462
3SS1-1191-119
4TT1-1201-120
RefinementHighest resolution: 1.74 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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