+Open data
-Basic information
Entry | Database: PDB / ID: 6owf | ||||||
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Title | Structure of a synthetic beta-carboxysome shell, T=3 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / BACTERIAL MICROCOMPARTMENTS / CARBOXYSOME | ||||||
Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis Similarity search - Function | ||||||
Biological species | Halothece sp. | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Sutter, M. / Laughlin, T.G. / Davies, K.M. / Kerfeld, C.A. | ||||||
Citation | Journal: Plant Physiol / Year: 2019 Title: Structure of a Synthetic -Carboxysome Shell. Authors: Markus Sutter / Thomas G Laughlin / Nancy B Sloan / Daniel Serwas / Karen M Davies / Cheryl A Kerfeld / Abstract: Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of ...Carboxysomes are capsid-like, CO-fixing organelles that are present in all cyanobacteria and some chemoautotrophs and that substantially contribute to global primary production. They are composed of a selectively permeable protein shell that encapsulates Rubisco, the principal CO-fixing enzyme, and carbonic anhydrase. As the centerpiece of the carbon-concentrating mechanism, by packaging enzymes that collectively enhance catalysis, the carboxysome shell enables the generation of a locally elevated concentration of substrate CO and the prevention of CO escape. A functional carboxysome consisting of an intact shell and cargo is essential for cyanobacterial growth under ambient CO concentrations. Using cryo-electron microscopy, we have determined the structure of a recombinantly produced simplified β-carboxysome shell. The structure reveals the sidedness and the specific interactions between the carboxysome shell proteins. The model provides insight into the structural basis of selective permeability of the carboxysome shell and can be used to design modifications to investigate the mechanisms of cargo encapsulation and other physiochemical properties such as permeability. Notably, the permeability properties are of great interest for modeling and evaluating this carbon-concentrating mechanism in metabolic engineering. Moreover, we find striking similarity between the carboxysome shell and the structurally characterized, evolutionarily distant metabolosome shell, implying universal architectural principles for bacterial microcompartment shells. | ||||||
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 | 6owf.cif.gz | 2.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6owf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6owf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/6owf ftp://data.pdbj.org/pub/pdb/validation_reports/ow/6owf | HTTPS FTP |
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-Related structure data
Related structure data | 20208MC 6owgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10275 (Title: Structure of a synthetic beta-carboxysome shell / Data size: 423.5 Data #1: Unaligned multiframe micrographs for synthetic carboxysome shells [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 12163.887 Da / Num. of mol.: 120 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothece sp. (strain PCC 7418) (bacteria) Strain: PCC 7418 / Gene: PCC7418_3532 / Production host: Escherichia coli (E. coli) / References: UniProt: K9YHS7 #2: Protein | Mass: 11509.216 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothece sp. (strain PCC 7418) (bacteria) Strain: PCC 7418 / Gene: PCC7418_3533 / Production host: Escherichia coli (E. coli) / References: UniProt: K9YFK1 |
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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: Synthetic beta-carboxysome shell (T=3) / Type: COMPLEX / Details: bacterial microcompartment shell / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Halothece sp. PCC 7418 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Conc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot for 6 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 56000 X / Nominal defocus min: 500 nm / Calibrated defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 6 sec. / Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1343 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 25 eV |
Image scans | Movie frames/image: 25 / Used frames/image: 1-25 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 47121 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1586 / Symmetry type: POINT |