+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10046 | |||||||||
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Title | Needle complex of the Shigella type 3 secretion system | |||||||||
Map data | Masked C1 reconstruction of needle complex of the Shigella type 3 secretion system, post-refined sharpened (b=-162), low-pass filtered at 5.11 A. | |||||||||
Sample |
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Function / homology | Function and homology information type III protein secretion system complex / protein secretion by the type III secretion system / protein secretion / protein targeting / cell surface / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Shigella flexneri (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.11 Å | |||||||||
Authors | Lunelli M / Kamprad A | |||||||||
Funding support | 2 items
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Citation | Journal: PLoS Pathog / Year: 2020 Title: Cryo-EM structure of the Shigella type III needle complex. Authors: Michele Lunelli / Antje Kamprad / Jörg Bürger / Thorsten Mielke / Christian M T Spahn / Michael Kolbe / Abstract: The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram- ...The Type III Secretion Systems (T3SS) needle complex is a conserved syringe-shaped protein translocation nanomachine with a mass of about 3.5 MDa essential for the survival and virulence of many Gram-negative bacterial pathogens. This system is composed of a membrane-embedded basal body and an extracellular needle that deliver effector proteins into host cells. High-resolution structures of the T3SS from different organisms and infection stages are needed to understand the underlying molecular mechanisms of effector translocation. Here, we present the cryo-electron microscopy structure of the isolated Shigella T3SS needle complex. The inner membrane (IM) region of the basal body adopts 24-fold rotational symmetry and forms a channel system that connects the bacterial periplasm with the export apparatus cage. The secretin oligomer adopts a heterogeneous architecture with 16- and 15-fold cyclic symmetry in the periplasmic N-terminal connector and C-terminal outer membrane ring, respectively. Two out of three IM subunits bind the secretin connector via a β-sheet augmentation. The cryo-EM map also reveals the helical architecture of the export apparatus core, the inner rod, the needle and their intervening interfaces. | |||||||||
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_10046.map.gz | 37 MB | EMDB map data format | |
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Header (meta data) | emd-10046-v30.xml emd-10046.xml | 17.4 KB 17.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10046_fsc.xml | 17.1 KB | Display | FSC data file |
Images | emd_10046.png | 43.1 KB | ||
Masks | emd_10046_msk_1.map | 421.9 MB | Mask map | |
Others | emd_10046_half_map_1.map.gz emd_10046_half_map_2.map.gz | 337.7 MB 338.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10046 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10046 | HTTPS FTP |
-Validation report
Summary document | emd_10046_validation.pdf.gz | 360.2 KB | Display | EMDB validaton report |
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Full document | emd_10046_full_validation.pdf.gz | 359.3 KB | Display | |
Data in XML | emd_10046_validation.xml.gz | 22.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10046 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10046 | HTTPS FTP |
-Related structure data
Related structure data | 6rwyMC 6rwkC 6rwxC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10046.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Masked C1 reconstruction of needle complex of the Shigella type 3 secretion system, post-refined sharpened (b=-162), low-pass filtered at 5.11 A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.38369 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_10046_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map.
File | emd_10046_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map.
File | emd_10046_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Needle complex of the Shigella type 3 secretion system
Entire | Name: Needle complex of the Shigella type 3 secretion system |
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Components |
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-Supramolecule #1: Needle complex of the Shigella type 3 secretion system
Supramolecule | Name: Needle complex of the Shigella type 3 secretion system type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Reconstruction of isolated needle complex without imposing symmetry |
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Source (natural) | Organism: Shigella flexneri (bacteria) / Strain: M90T / Location in cell: Membrane |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 5.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV Details: Sample applied on grid 5 ul, incubation time 5 min on ice, then moved into Vitrobot and 5 ul sample applied again. Blot time: 2 sec Blot force: -2 Drain time: 0 sec. |
Details | Isolated needle complex in detergent solution |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 5238 / Average exposure time: 1.5 sec. / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.0015 µm / Nominal magnification: 101179 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Overall B value: 162 |
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Output model | PDB-6rwy: |