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Yorodumi- EMDB-30782: The Shigella flexneri type III secretion system tip complex by cr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30782 | |||||||||
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Title | The Shigella flexneri type III secretion system tip complex by cryo-electron microscopy | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Shigella flexneri (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 10.4 Å | |||||||||
Authors | Cheung M / Taba S / Villar-Briones A / Hall M / Shintake T | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: To Be Published Title: The Shigella flexneri type III secretion system tip complex by cryo-electron microscopy Authors: Cheung M / Taba S / Villar-Briones A / Hall M / Shintake T | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30782.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-30782-v30.xml emd-30782.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30782_fsc.xml | 9.3 KB | Display | FSC data file |
Images | emd_30782.png | 33.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30782 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30782 | HTTPS FTP |
-Validation report
Summary document | emd_30782_validation.pdf.gz | 316.7 KB | Display | EMDB validaton report |
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Full document | emd_30782_full_validation.pdf.gz | 316.3 KB | Display | |
Data in XML | emd_30782_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | emd_30782_validation.cif.gz | 12.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30782 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30782 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_30782.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Tip complex of the Shigella flexneri type III secretion system
Entire | Name: Tip complex of the Shigella flexneri type III secretion system |
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Components |
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-Supramolecule #1: Tip complex of the Shigella flexneri type III secretion system
Supramolecule | Name: Tip complex of the Shigella flexneri type III secretion system type: complex / ID: 1 / Parent: 0 Details: Tip complex analysed from purified needle complexes, the main structural component of the type III secretion system |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Details: 150 mM NaCl, 10 mM Tris-HCl pH 8, 0.2% (w/v) n-dodecyl-B-D-maltoside |
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Double-sided blotting graphene oxide grid preparation method (Cheung et al., 2018).. |
Details | Needle complexes dispersed in vitreous ice films using the double-blotting graphene oxide procedure (Cheung et al., 2018) |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 45000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |