+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1656 | |||||||||
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Title | Control structure of the RbcL8 octamer | |||||||||
Map data | This is cryo-EM map of the rubisco large subunit octamer | |||||||||
Sample |
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Keywords | photosynthesis / protein folding / Rubisco / Rubisco assembly / chaperones | |||||||||
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) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Liu C / Young A / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Rao KV / Berninghausen O / Mielke T / Hartl FU ...Liu C / Young A / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Rao KV / Berninghausen O / Mielke T / Hartl FU / 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1656.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-1656-v30.xml emd-1656.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_1656.jpg | 66 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1656 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1656 | HTTPS FTP |
-Validation report
Summary document | emd_1656_validation.pdf.gz | 193.3 KB | Display | EMDB validaton report |
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Full document | emd_1656_full_validation.pdf.gz | 192.4 KB | Display | |
Data in XML | emd_1656_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1656 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1656 | HTTPS FTP |
-Related structure data
Related structure data | 2wvwMC 1654C 1655C 3hybC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1656.map.gz / Format: CCP4 / Size: 5.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is cryo-EM map of the rubisco large subunit octamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rubisco large subnuit octamer
Entire | Name: Rubisco large subnuit octamer |
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Components |
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-Supramolecule #1000: Rubisco large subnuit octamer
Supramolecule | Name: Rubisco large subnuit octamer / type: sample / ID: 1000 / Oligomeric state: Octamer / Number unique components: 1 |
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Molecular weight | Theoretical: 420 KDa |
-Macromolecule #1: RbcL
Macromolecule | Name: RbcL / type: protein_or_peptide / ID: 1 / Name.synonym: Rubisco large subunit / Number of copies: 8 / Oligomeric state: Octamer / Recombinant expression: Yes |
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Source (natural) | Organism: Synechococcus elongatus (bacteria) / Strain: PCC 6301 |
Molecular weight | Theoretical: 52.5 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant plasmid: pet11a |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8.7 / Details: 20 mM Tris-HCl, pH 8.7 |
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Staining | Type: NEGATIVE / Details: cryo-EM |
Grid | Details: Quantifoil grids (3/3) with 2 nm carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 85 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot Method: 10 second blotting before plunging, used 2 layers of filter paper |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Temperature | Average: 95 K |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (2k x 2k) / Digitization - Sampling interval: 3.308 µm / Average electron dose: 20 e/Å2 / Details: Data collected on CCD / Bits/pixel: 16 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 90000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 90000 |
Sample stage | Specimen holder: single tilt cryo holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Applied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 13217 |
Final angle assignment | Details: EMAN |