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Yorodumi- EMDB-6477: Identification and characterization of multiple Rubisco activases... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6477 | |||||||||
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Title | Identification and characterization of multiple Rubisco activases in chemoautotrophic bacteria | |||||||||
Map data | Reconstruction of AfQ2 | |||||||||
Sample |
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Keywords | Rubisco / activase | |||||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 23.0 Å | |||||||||
Authors | Tsai Y-CC / Lapina MC / Mueller-Cajar O / Bhushan S | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Identification and characterization of multiple rubisco activases in chemoautotrophic bacteria. Authors: Yi-Chin Candace Tsai / Maria Claribel Lapina / Shashi Bhushan / Oliver Mueller-Cajar / Abstract: Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is responsible for almost all biological CO2 assimilation, but forms inhibited complexes with its substrate ribulose-1,5-bisphosphate (RuBP) ...Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is responsible for almost all biological CO2 assimilation, but forms inhibited complexes with its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates. The distantly related AAA+ proteins rubisco activase and CbbX remodel inhibited rubisco complexes to effect inhibitor release in plants and α-proteobacteria, respectively. Here we characterize a third class of rubisco activase in the chemolithoautotroph Acidithiobacillus ferrooxidans. Two sets of isoforms of CbbQ and CbbO form hetero-oligomers that function as specific activases for two structurally diverse rubisco forms. Mutational analysis supports a model wherein the AAA+ protein CbbQ functions as motor and CbbO is a substrate adaptor that binds rubisco via a von Willebrand factor A domain. Understanding the mechanisms employed by nature to overcome rubisco's shortcomings will increase our toolbox for engineering photosynthetic carbon dioxide fixation. | |||||||||
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_6477.map.gz | 614.5 KB | EMDB map data format | |
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Header (meta data) | emd-6477-v30.xml emd-6477.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | 400_6477.gif 80_6477.gif | 21.2 KB 2.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6477 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6477 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6477.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of AfQ2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.11 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 : AfQ2
Entire | Name: AfQ2 |
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Components |
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-Supramolecule #1000: AfQ2
Supramolecule | Name: AfQ2 / type: sample / ID: 1000 / Oligomeric state: Hexamer / Number unique components: 1 |
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Molecular weight | Experimental: 173 KDa / Theoretical: 181 KDa / Method: sedimentation and gel filtration |
-Macromolecule #1: RuBisCo activase
Macromolecule | Name: RuBisCo activase / type: protein_or_peptide / ID: 1 / Name.synonym: CbbQ / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Acidithiobacillus ferrooxidans (bacteria) / synonym: Chemoautotrophic bacteria / Location in cell: Cytosol |
Molecular weight | Experimental: 173 KDa / Theoretical: 181 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: BL21 / Recombinant plasmid: pHue |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 8 / Details: 50 mM NaCl, 20 mM Tris-HCl, 5 mM Mg-ATP |
Staining | Type: NEGATIVE Details: Negative stain, 2% w/v uranyl acetate for 30 seconds |
Grid | Details: 200 mesh Cu grid with thin carbon support, glow discharged |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 66350 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 6.3 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 43000 |
Sample stage | Specimen holder model: OTHER |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 66,000 times magnification. |
Date | Apr 29, 2014 |
Image recording | Category: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 110 / Average electron dose: 20 e/Å2 |
-Image processing
CTF correction | Details: Each particle |
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Final two d classification | Number classes: 20 |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 958 |
Details | EMAN2 |