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Yorodumi- EMDB-3217: In situ sub-tomogram average of the host-contact Chlamydia tracho... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3217 | |||||||||
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Title | In situ sub-tomogram average of the host-contact Chlamydia trachomatis type III secretion system | |||||||||
Map data | Sub-tomogram average of Chlamydia trachomatis type III secretion system (host-contact) | |||||||||
Sample |
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Keywords | injectisome / type III secretion / T3SS | |||||||||
Biological species | Chlamydia trachomatis (bacteria) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 38.0 Å | |||||||||
Authors | Nans A / Kudryashev M / Saibil HR / Hayward RD | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure of a bacterial type III secretion system in contact with a host membrane in situ. Authors: Andrea Nans / Mikhail Kudryashev / Helen R Saibil / Richard D Hayward / Abstract: Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact ...Many bacterial pathogens of animals and plants use a conserved type III secretion system (T3SS) to inject virulence effector proteins directly into eukaryotic cells to subvert host functions. Contact with host membranes is critical for T3SS activation, yet little is known about T3SS architecture in this state or the conformational changes that drive effector translocation. Here we use cryo-electron tomography and sub-tomogram averaging to derive the intact structure of the primordial Chlamydia trachomatis T3SS in the presence and absence of host membrane contact. Comparison of the averaged structures demonstrates a marked compaction of the basal body (4 nm) occurs when the needle tip contacts the host cell membrane. This compaction is coupled to a stabilization of the cytosolic sorting platform-ATPase. Our findings reveal the first structure of a bacterial T3SS from a major human pathogen engaged with a eukaryotic host, and reveal striking 'pump-action' conformational changes that underpin effector injection. | |||||||||
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_3217.map.gz | 40.7 MB | EMDB map data format | |
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Header (meta data) | emd-3217-v30.xml emd-3217.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | EMD-3217_snapshot2_500.tif | 978.8 KB | ||
Others | emd_3217_additional_1.map.gz | 129.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3217 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3217 | HTTPS FTP |
-Validation report
Summary document | emd_3217_validation.pdf.gz | 196.4 KB | Display | EMDB validaton report |
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Full document | emd_3217_full_validation.pdf.gz | 195.5 KB | Display | |
Data in XML | emd_3217_validation.xml.gz | 6.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3217 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3217 | HTTPS FTP |
-Related structure data
Related structure data | 3216C C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10048 (Title: Cryo-electron tomogram of Chlamydia trachomatis with type III secretion system in contact with HeLa cell Data size: 13.6 Data #1: Aligned multi-frame micrographs that comprise a tilt series of Chlamydia trachomatis type III secretion systems in contact with a HeLa cell [class averages]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3217.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sub-tomogram average of Chlamydia trachomatis type III secretion system (host-contact) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 3217 additional 1.map
File | emd_3217_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Chlamydia trachomatis type III secretion system (host-contact)
Entire | Name: Chlamydia trachomatis type III secretion system (host-contact) |
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Components |
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-Supramolecule #1000: Chlamydia trachomatis type III secretion system (host-contact)
Supramolecule | Name: Chlamydia trachomatis type III secretion system (host-contact) type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Chlamydia trachomatis type III secretion system
Supramolecule | Name: Chlamydia trachomatis type III secretion system / type: organelle_or_cellular_component / ID: 1 Details: Type III secretion systems were imaged in contact with U2OS or HeLa cells grown directly on EM grids. Recombinant expression: No |
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Source (natural) | Organism: Chlamydia trachomatis (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | cell |
-Sample preparation
Grid | Details: 200 mesh gold Quantifoil 3.5/1 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 6-10 seconds before plunging. |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Specialist optics | Energy filter - Name: Gatan Quantum / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV |
Date | Nov 10, 2014 |
Image recording | Category: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: -10.0 µm / Nominal magnification: 41000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 60 ° |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Sub-tomograms were selected in IMOD and cropped in Dynamo. Alignment and averaging was carried out in Dynamo. |
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Final reconstruction | Applied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 196 |
CTF correction | Details: Each micrograph was phase-flipped in IMOD using the measured defocus |