+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-18710 | |||||||||
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Title | Tomogram of P. tricornutum pyrenoid | |||||||||
Map data | ||||||||||
Sample |
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Keywords | marine diatoms / chloroplast / pyrenoid / photosynthesis / carbon fixation / rubisco | |||||||||
Biological species | Thalassiosira pseudonana (Diatom) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Demulder M / Righetto RD / Wietrzynski W / Lamm L / Engel BD | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Cell(Cambridge,Mass.) / Year: 2024 Title: Diatom pyrenoids are encased in a protein shell that enables efficient CO2 fixation Authors: Demulder M / Engel BD / Shimakawa G / Flori S / Kawamoto A / Tsuji Y / Nawaly H / Tanaka A / Tohda R / Ota T / Matsui H / Morishima N / Okubo R / Wietrzynski W / Lamm L / Righetto RD / ...Authors: Demulder M / Engel BD / Shimakawa G / Flori S / Kawamoto A / Tsuji Y / Nawaly H / Tanaka A / Tohda R / Ota T / Matsui H / Morishima N / Okubo R / Wietrzynski W / Lamm L / Righetto RD / Uwizeye C / Gallet B / Jouneau P-H / Gerle C / Kurisu G / Finazzi G / Matsuda Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_18710.map.gz | 1.5 GB | EMDB map data format | |
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Header (meta data) | emd-18710-v30.xml emd-18710.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_18710.png | 31 KB | ||
Filedesc metadata | emd-18710.cif.gz | 3.8 KB | ||
Others | emd_18710_additional_1.map.gz | 355.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-18710 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18710 | HTTPS FTP |
-Validation report
Summary document | emd_18710_validation.pdf.gz | 698.7 KB | Display | EMDB validaton report |
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Full document | emd_18710_full_validation.pdf.gz | 698.3 KB | Display | |
Data in XML | emd_18710_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_18710_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18710 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18710 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_18710.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.08 Å | ||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_18710_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : T. pseudonana
Entire | Name: T. pseudonana (Diatom) |
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Components |
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-Supramolecule #1: T. pseudonana
Supramolecule | Name: T. pseudonana / type: cell / ID: 1 / Parent: 0 / Details: Pyrenoid in T. pseudonana chloroplast |
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Source (natural) | Organism: Thalassiosira pseudonana (Diatom) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 3 / Focused ion beam - Current: 0.03 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 83 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is FEI Aquilos II. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 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: 3.5 µm / Nominal defocus min: 3.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 53 |
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