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Yorodumi- PDB-8cmy: Structure of the Cyanobium sp. PCC 7001 determined with C1 symmetry -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cmy | |||||||||
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Title | Structure of the Cyanobium sp. PCC 7001 determined with C1 symmetry | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Carboxysome / Carbon fixation / cyanobacteria | |||||||||
Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Cyanobium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.79 Å | |||||||||
Authors | Evans, S.L. / Bergeron, J.R.C. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2023 Title: Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Authors: Sasha L Evans / Monsour M J Al-Hazeem / Daniel Mann / Nicolas Smetacek / Andrew J Beavil / Yaqi Sun / Taiyu Chen / Gregory F Dykes / Lu-Ning Liu / Julien R C Bergeron / Abstract: Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, ...Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cmy.cif.gz | 888.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cmy.ent.gz | 624.9 KB | Display | PDB format |
PDBx/mmJSON format | 8cmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cmy_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8cmy_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8cmy_validation.xml.gz | 126.1 KB | Display | |
Data in CIF | 8cmy_validation.cif.gz | 187.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/8cmy ftp://data.pdbj.org/pub/pdb/validation_reports/cm/8cmy | HTTPS FTP |
-Related structure data
Related structure data | 7yyoC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 52526.531 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Cyanobium (bacteria) References: UniProt: A5CKD0, ribulose-bisphosphate carboxylase #2: Protein | Mass: 12967.611 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Cyanobium (bacteria) References: UniProt: A0A182AM64, ribulose-bisphosphate carboxylase #3: Sugar | ChemComp-CAP / #4: Chemical | ChemComp-MG / Has ligand of interest | N | |
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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: Carboxysome / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Cyanobium (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131356 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.81 Å2 | ||||||||||||||||||||||||
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