+Open data
-Basic information
Entry | Database: PDB / ID: 7ckc | ||||||
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Title | Simplified Alpha-Carboxysome, T=4 | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / Bacterial Microcompartment / Alpha-carboxysome | ||||||
Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / carbon fixation Similarity search - Function | ||||||
Biological species | Halothiobacillus neapolitanus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Tan, Y.Q. / Ali, S. / Xue, B. / Robinson, R.C. / Narita, A. / Yew, W.S. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Biomacromolecules / Year: 2021 Title: Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization. Authors: Yong Quan Tan / Samson Ali / Bo Xue / Wei Zhe Teo / Lay Hiang Ling / Maybelle Kho Go / Hong Lv / Robert C Robinson / Akihiro Narita / Wen Shan Yew / Abstract: Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged ...Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries. | ||||||
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 | 7ckc.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ckc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ckc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ckc_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7ckc_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 7ckc_validation.xml.gz | 405 KB | Display | |
Data in CIF | 7ckc_validation.cif.gz | 653.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/7ckc ftp://data.pdbj.org/pub/pdb/validation_reports/ck/7ckc | HTTPS FTP |
-Related structure data
Related structure data | 30385MC 7ckbC 7dhqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 10173.640 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria) Production host: Escherichia coli (E. coli) / References: UniProt: O85043 #2: Protein | Mass: 9973.478 Da / Num. of mol.: 180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria) Strain: ATCC 23641 / c2 / Gene: csoS1A, Hneap_0915 / Production host: Escherichia coli (E. coli) / References: UniProt: P45689 |
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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: Simplified Alpha-Carboxysome, T=4 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 2.3 MDa / Experimental value: NO |
Source (natural) | Organism: Halothiobacillus neapolitanus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-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 FIELD |
Image recording | Electron dose: 64.3 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 94129 | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67192 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||
Atomic model building |
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