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Yorodumi- EMDB-14625: Subtomogram averaging of Rubisco from Cyanobium carboxysome (oute... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14625 | ||||||||||||
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Title | Subtomogram averaging of Rubisco from Cyanobium carboxysome (outerlayer) | ||||||||||||
Map data | main map from cisTEM reconstruction within emClarity package, postprocessed with relion | ||||||||||||
Sample |
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Biological species | Cyanobium sp. PCC 7001 (bacteria) | ||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 4.28 Å | ||||||||||||
Authors | Ni T / Zhu Y / Seaton-Burn W / Zhang P | ||||||||||||
Funding support | United Kingdom, European Union, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structure and assembly of cargo Rubisco in two native α-carboxysomes. Authors: Tao Ni / Yaqi Sun / Will Burn / Monsour M J Al-Hazeem / Yanan Zhu / Xiulian Yu / Lu-Ning Liu / Peijun Zhang / Abstract: Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase ...Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14625.map.gz | 31 MB | EMDB map data format | |
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Header (meta data) | emd-14625-v30.xml emd-14625.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14625_fsc.xml | 7.4 KB | Display | FSC data file |
Images | emd_14625.png | 99.4 KB | ||
Others | emd_14625_half_map_1.map.gz emd_14625_half_map_2.map.gz | 20.2 MB 20.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14625 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14625 | HTTPS FTP |
-Validation report
Summary document | emd_14625_validation.pdf.gz | 779.9 KB | Display | EMDB validaton report |
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Full document | emd_14625_full_validation.pdf.gz | 779.4 KB | Display | |
Data in XML | emd_14625_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_14625_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14625 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14625 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_14625.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map from cisTEM reconstruction within emClarity package, postprocessed with relion | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: emClarity half map 1 from cisTEM reconstruction
File | emd_14625_half_map_1.map | ||||||||||||
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Annotation | emClarity half map 1 from cisTEM reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: emClarity half map 1 from cisTEM reconstruction
File | emd_14625_half_map_2.map | ||||||||||||
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Annotation | emClarity half map 1 from cisTEM reconstruction | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of Rubisco within Cyanobium carboxysome
Entire | Name: Structure of Rubisco within Cyanobium carboxysome |
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Components |
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-Supramolecule #1: Structure of Rubisco within Cyanobium carboxysome
Supramolecule | Name: Structure of Rubisco within Cyanobium carboxysome / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Cyanobium sp. PCC 7001 (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.65 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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