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Yorodumi- EMDB-11907: In situ subtomogram averaging structure of the type III secretion... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11907 | |||||||||
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Title | In situ subtomogram averaging structure of the type III secretion system of yersinia enterocolitica - needle tip | |||||||||
Map data | Subtomogram average structure of the type III secretion system of yersinia enterocolitica - focused on the needle tip | |||||||||
Sample |
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Biological species | Yersinia enterocolitica (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 39.0 Å | |||||||||
Authors | Berger C / Ravelli RBG / Lopez-Iglesias C / Kudryashev M / Diepold A / Peters PJ | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: J Struct Biol / Year: 2021 Title: Structure of the Yersinia injectisome in intracellular host cell phagosomes revealed by cryo FIB electron tomography. Authors: Casper Berger / Raimond B G Ravelli / Carmen López-Iglesias / Mikhail Kudryashev / Andreas Diepold / Peter J Peters / Abstract: Many pathogenic bacteria use the type III secretion system (T3SS), or injectisome, to secrete toxins into host cells. These protruding systems are primary targets for drug and vaccine development. ...Many pathogenic bacteria use the type III secretion system (T3SS), or injectisome, to secrete toxins into host cells. These protruding systems are primary targets for drug and vaccine development. Upon contact between injectisomes and host membranes, toxin secretion is triggered. How this works structurally and functionally is yet unknown. Using cryo-focused ion beam milling and cryo-electron tomography, we visualized injectisomes of Yersinia enterocolitica inside the phagosomes of infected human myeloid cells in a close-to-native state. We observed that a minimum needle length is required for injectisomes to contact the host membrane and bending of host membranes by some injectisomes that contact the host. Through subtomogram averaging, the structure of the entire injectisome was determined, which revealed structural differences in the cytosolic sorting platform compared to other bacteria. These findings contribute to understanding how injectisomes secrete toxins into host cells and provides the indispensable native context. The application of these cryo-electron microscopy techniques paves the way for the study of the 3D structure of infection-relevant protein complexes in host-pathogen interactions. | |||||||||
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_11907.map.gz | 15.6 MB | EMDB map data format | |
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Header (meta data) | emd-11907-v30.xml emd-11907.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11907_fsc.xml | 6.3 KB | Display | FSC data file |
Images | emd_11907.png | 77.8 KB | ||
Masks | emd_11907_msk_1.map | 16.8 MB | Mask map | |
Others | emd_11907_additional_1.map.gz emd_11907_half_map_1.map.gz emd_11907_half_map_2.map.gz | 15.6 MB 15.6 MB 15.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11907 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11907 | HTTPS FTP |
-Validation report
Summary document | emd_11907_validation.pdf.gz | 718.9 KB | Display | EMDB validaton report |
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Full document | emd_11907_full_validation.pdf.gz | 718 KB | Display | |
Data in XML | emd_11907_validation.xml.gz | 11.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11907 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11907 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11907.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Subtomogram average structure of the type III secretion system of yersinia enterocolitica - focused on the needle tip | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.452 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11907_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Subtomogram average structure of the type III secretion...
File | emd_11907_additional_1.map | ||||||||||||
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Annotation | Subtomogram average structure of the type III secretion system of yersinia enterocolitica - focused on the needle tip, filtered to 3.9 nm resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of the odd particles
File | emd_11907_half_map_1.map | ||||||||||||
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Annotation | half map of the odd particles | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map of the even particles
File | emd_11907_half_map_2.map | ||||||||||||
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Annotation | half map of the even particles | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sorting platform of the Type III secretion system of Yersinia ent...
Entire | Name: Sorting platform of the Type III secretion system of Yersinia enterocolitica |
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Components |
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-Supramolecule #1: Sorting platform of the Type III secretion system of Yersinia ent...
Supramolecule | Name: Sorting platform of the Type III secretion system of Yersinia enterocolitica type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Yersinia enterocolitica (bacteria) / Strain: E40 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 Details: CElls were grown in RPMI 1640 medium on the grid. 2 ul of RPMI 1640 was applied to the grid just prior to vitrification |
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Grid | Model: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 310 K / Instrument: HOMEMADE PLUNGER Details: FEI vitrobot modified with a jet-vitrification module and a blotforce feedback mechanism.. |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average exposure time: 24.0 sec. / Average electron dose: 2.86 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 min: -0.005 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |