+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-1654 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Rubisco RbcL8-RbcX2-8 complex | |||||||||
![]() | This is a negative stain 3D reconstruction of a Rubisco assembly intermediate comprising eight copies of the large subunit RbcL and eight copies of the assembly chaperone RbcX2. | |||||||||
![]() |
| |||||||||
![]() | Photosynthesis / protein folding / Rubisco / Rubisco assembly / chaperones | |||||||||
Function / homology | ![]() ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity ...ribulose bisphosphate carboxylase complex assembly / carboxysome / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / photosynthesis / protein folding chaperone / monooxygenase activity / magnesium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 17.0 Å | |||||||||
![]() | Liu C / Young AL / Starling-Windhof A / Bracher A / Saschenbrecker S / Rao BV / Berninghausen O / Mielke T / Hartl FU / Beckmann R / Hayer-Hartl M | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 995.7 KB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 11.3 KB 11.3 KB | Display Display | ![]() |
Images | ![]() ![]() | 75.1 KB 64 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wvwMC ![]() 1655C ![]() 1656C ![]() 3hybC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | This is a negative stain 3D reconstruction of a Rubisco assembly intermediate comprising eight copies of the large subunit RbcL and eight copies of the assembly chaperone RbcX2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.308 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
-Entire : RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the...
Entire | Name: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the large Rubisco subunit RbcL and eight copies of the dimeric assembly chaperone RbcX2. |
---|---|
Components |
|
-Supramolecule #1000: RbcL8-X8 Rubisco assembly intermediate containing 8 copies of the...
Supramolecule | 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: sample / ID: 1000 Oligomeric state: one RbcL-octamer binds to on RbcX2 octamer Number unique components: 2 |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 52.5 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: RbcX
Macromolecule | Name: RbcX / type: protein_or_peptide / ID: 2 / Name.synonym: RbcX / Number of copies: 16 / Oligomeric state: Dimer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 30.4 KDa |
Recombinant expression | Organism: Eschericia coli BL21(DE3) / Recombinant plasmid: pet28b |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 8.7 / Details: 20 mM Tris-HCl, pH 8.7 |
---|---|
Staining | Type: NEGATIVE / Details: Uranyl acetate |
Grid | Details: Quantifoil grids (3/3) with 2 nm carbon on top |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-
Electron microscopy
Microscope | FEI TECNAI 12 |
---|---|
Temperature | Average: 293 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 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 90000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 90000 |
Sample stage | Specimen holder: Single tilt tomography holder / Specimen holder model: GATAN LIQUID NITROGEN |
-
Image processing
CTF correction | Details: Each particle |
---|---|
Final reconstruction | Applied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1 / Number images used: 2809 |
Final angle assignment | Details: EMAN1 |