+Open data
-Basic information
Entry | Database: PDB / ID: 2wvw | ||||||
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Title | Cryo-EM structure of the RbcL-RbcX complex | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / COMPLEX ASSEMBLY / PHOTORESPIRATION / DISULFIDE BOND / CARBON FIXATION / LYASE / CHAPERONE / CALVIN CYCLE / CARBON DIOXIDE FIXATION / MONOOXYGENASE / METAL-BINDING / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / photorespiration / carboxysome / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / carbon fixation / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | SYNECHOCOCCUS ELONGATUS (bacteria) ANABAENA SP. CA (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9 Å | ||||||
Authors | Liu, C. / Young, A.L. / Starling-Windhof, A. / Bracher, A. / Saschenbrecker, S. / Rao, B.V. / Rao, K.V. / Berninghausen, O. / Mielke, T. / Hartl, F.U. ...Liu, C. / Young, A.L. / Starling-Windhof, A. / Bracher, A. / Saschenbrecker, S. / Rao, B.V. / Rao, K.V. / Berninghausen, O. / Mielke, T. / Hartl, F.U. / Beckmann, R. / Hayer-Hartl, M. | ||||||
Citation | Journal: Nature / Year: 2010 Title: Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich ...Authors: Cuimin Liu / Anna L Young / Amanda Starling-Windhof / Andreas Bracher / Sandra Saschenbrecker / Bharathi Vasudeva Rao / Karnam Vasudeva Rao / Otto Berninghausen / Thorsten Mielke / F Ulrich Hartl / Roland Beckmann / Manajit Hayer-Hartl / Abstract: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The ...Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2wvw.cif.gz | 903.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wvw.ent.gz | 721.4 KB | Display | PDB format |
PDBx/mmJSON format | 2wvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wvw_validation.pdf.gz | 1020.6 KB | Display | wwPDB validaton report |
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Full document | 2wvw_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 2wvw_validation.xml.gz | 171.3 KB | Display | |
Data in CIF | 2wvw_validation.cif.gz | 232.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/2wvw ftp://data.pdbj.org/pub/pdb/validation_reports/wv/2wvw | HTTPS FTP |
-Related structure data
Related structure data | 1654MC 1655MC 1656MC 3hybC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52516.605 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNECHOCOCCUS ELONGATUS (bacteria) / Strain: PCC 6301 / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: P00880, ribulose-bisphosphate carboxylase #2: Protein | Mass: 17694.930 Da / Num. of mol.: 16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. CA (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q44212 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RBCL8-X8 RUBISCO ASSEMBLY INTERMEDIATE CONTAINING 8 COPIES OF THE LARGE RUBISCO SUBUNIT RBCL AND EIGHT COPIES OF THE DIMERIC ASSEMBLY CHAPERONE RBCX2. Type: COMPLEX |
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Buffer solution | Name: 20 MM TRIS-HCL, PH 8.7 / pH: 8.7 / Details: 20 MM TRIS-HCL, PH 8.7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: QUANTIFOIL GRIDS (3/3) WITH 2 NM CARBON ON TOP / Grid type: Quantifoil R3/3 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: VITROBOT USED, LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38900 X / Nominal defocus max: 3100 nm / Nominal defocus min: 1000 nm / Cs: 2.26 mm |
Specimen holder | Temperature: 85 K / Tilt angle max: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 56 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: EMAN / Version: 1 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: EACH PARTICLE | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: STANDARD EMAN REFINE PROCEDURE / Resolution: 9 Å / Num. of particles: 11104 / Nominal pixel size: 1.63 Å / Actual pixel size: 1.63 Å / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Details: METHOD--MANUAL | ||||||||||||
Atomic model building | PDB-ID: 3HYB Accession code: 3HYB / Source name: PDB / Type: experimental model | ||||||||||||
Refinement | Highest resolution: 9 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 9 Å
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