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Yorodumi- EMDB-1655: Coupled chaperone action in folding and assembly of hexadecameric... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1655 | |||||||||
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Title | Coupled chaperone action in folding and assembly of hexadecameric Rubisco | |||||||||
Map data | This is a cryo-EM map of the RbcL8-X8 assembly intermediate | |||||||||
Sample |
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Keywords | Photosynthesis / protein folding / Rubisco / Rubisco assembly / chaperones | |||||||||
Function / homology | Function and homology information ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | Synechococcus elongatus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 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_1655.map.gz | 4 MB | EMDB map data format | |
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Header (meta data) | emd-1655-v30.xml emd-1655.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_1655.jpg | 85.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1655 | HTTPS FTP |
-Related structure data
Related structure data | 2wvwMC 1654C 1656C 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_1655.map.gz / Format: CCP4 / Size: 20.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryo-EM map of the RbcL8-X8 assembly intermediate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 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 assembly intermediate containing 8 copies of the large Ru...
Entire | Name: Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and 8 copies of the dimeric assembly chaperone RbcX2 |
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Components |
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-Supramolecule #1000: Rubisco assembly intermediate containing 8 copies of the large Ru...
Supramolecule | Name: Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and 8 copies of the dimeric assembly chaperone RbcX2 type: sample / ID: 1000 Oligomeric state: One RbcL-octamer binds to on RbcX2 octamer Number unique components: 1 |
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Molecular weight | Theoretical: 660 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 | 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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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 sec blottting before plunging, 2 layers of filter paper |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 95 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 1.63 µm / Average electron dose: 20 e/Å2 / Details: Scanned on Heidelberg Primescan at 4000 dpi / Od range: 1.2 / Bits/pixel: 16 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.1 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: FEI Polara cartridge system / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-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: 9.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 11104 |
Final angle assignment | Details: EMAN |