+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44416 | ||||||||||||
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Title | Binned tomogram of stationary phase Burkholderia thailandensis | ||||||||||||
Map data | Binned tomogram of stationary phase Burkholderia thailandensis | ||||||||||||
Sample |
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Keywords | stationary phase / CELL CYCLE | ||||||||||||
Biological species | Burkholderia thailandensis E264 (bacteria) | ||||||||||||
Method | electron tomography / cryo EM | ||||||||||||
Authors | Khanna K / Welch MD | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: MicroPubl Biol / Year: 2024 Title: Cryo-electron tomography of stationary phase . Authors: Kanika Khanna / Matthew D Welch / Abstract: species belonging to the pseudomallei group include significant human and animal pathogens as well as the non-pathogenic species . These bacteria co-opt the host cell machinery for their ... species belonging to the pseudomallei group include significant human and animal pathogens as well as the non-pathogenic species . These bacteria co-opt the host cell machinery for their replication and spread between host cells. Thus, it is of interest to understand the structural features of these cells that contribute to host cell colonization and virulence. This study provides high-resolution cryo-electron tomograms of stationary phase . It reveals the presence of compact nucleoids and storage granules, as well as examples of the type III secretion system and chemoreceptor arrays. The data can be used to investigate the near-atomic structure of stationary-phase bacterial macromolecules, such as ribosomes. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44416.map.gz | 179.9 MB | EMDB map data format | |
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Header (meta data) | emd-44416-v30.xml emd-44416.xml | 32.8 KB 32.8 KB | Display Display | EMDB header |
Images | emd_44416.png | 177.2 KB | ||
Filedesc metadata | emd-44416.cif.gz | 3.9 KB | ||
Others | emd_44416_additional_1.map.gz emd_44416_additional_10.map.gz emd_44416_additional_11.map.gz emd_44416_additional_12.map.gz emd_44416_additional_2.map.gz emd_44416_additional_3.map.gz emd_44416_additional_4.map.gz emd_44416_additional_5.map.gz emd_44416_additional_6.map.gz emd_44416_additional_7.map.gz emd_44416_additional_8.map.gz emd_44416_additional_9.map.gz | 170.1 MB 364.9 MB 335.4 MB 372.9 MB 321 MB 146.6 MB 156.3 MB 158.4 MB 129.6 MB 111.1 MB 269.3 MB 311.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44416 | HTTPS FTP |
-Validation report
Summary document | emd_44416_validation.pdf.gz | 571.2 KB | Display | EMDB validaton report |
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Full document | emd_44416_full_validation.pdf.gz | 570.8 KB | Display | |
Data in XML | emd_44416_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_44416_validation.cif.gz | 6.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44416 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44416 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44416.map.gz / Format: CCP4 / Size: 227 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Annotation | Binned tomogram of stationary phase Burkholderia thailandensis | ||||||||||||||||||||
Voxel size | X=Y=Z: 14.9 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
+Additional map: Binned tomogram of stationary phase Burkholderia thailandensis
-Sample components
-Entire : Cryo-electron tomography of stationary phase Burkholderia thailan...
Entire | Name: Cryo-electron tomography of stationary phase Burkholderia thailandensis |
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Components |
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-Supramolecule #1: Cryo-electron tomography of stationary phase Burkholderia thailan...
Supramolecule | Name: Cryo-electron tomography of stationary phase Burkholderia thailandensis type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Burkholderia thailandensis E264 (bacteria) |
-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: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 93 K / Focused ion beam - Initial thickness: 2000 / Focused ion beam - Final thickness: 150 Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. 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: GATAN K3 (6k x 4k) / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 40 |
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