+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5352 | |||||||||
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Title | Structure of a type III secretion needle | |||||||||
Map data | This is an reconstruction of the type III secretion needle | |||||||||
Sample |
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Keywords | type III secretion system / needle / helical filament | |||||||||
Function / homology | Function and homology information type III protein secretion system complex / protein secretion by the type III secretion system / : / cell surface / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Shigella flexneri (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.7 Å | |||||||||
Authors | Fujii T / Cheung M / Blanco A / Kato T / Blocker AJ / Namba K | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Structure of a type III secretion needle at 7-Å resolution provides insights into its assembly and signaling mechanisms. Authors: Takashi Fujii / Martin Cheung / Amandine Blanco / Takayuki Kato / Ariel J Blocker / Keiichi Namba / Abstract: Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the ...Type III secretion systems of Gram-negative bacteria form injection devices that deliver effector proteins into eukaryotic cells during infection. They span both bacterial membranes and the extracellular space to connect with the host cell plasma membrane. Their extracellular portion is a needle-like, hollow tube that serves as a secretion conduit for effector proteins. The needle of Shigella flexneri is approximately 50-nm long and 7-nm thick and is made by the helical assembly of one protein, MxiH. We provide a 7-Å resolution 3D image reconstruction of the Shigella needle by electron cryomicroscopy, which resolves α-helices and a β-hairpin that has never been observed in the crystal and solution structures of needle proteins, including MxiH. An atomic model of the needle based on the 3D-density map, in comparison with that of the bacterial-flagellar filament, provides insights into how such a thin tubular structure is stably assembled by intricate intermolecular interactions. The map also illuminates how the needle-length control protein functions as a ruler within the central channel during export of MxiH for assembly at the distal end of the needle, and how the secretion-activation signal may be transduced through a conformational change of the needle upon host-cell contact. | |||||||||
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_5352.map.gz | 3.6 MB | EMDB map data format | |
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Header (meta data) | emd-5352-v30.xml emd-5352.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | emd_5352_1.jpg | 61.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5352 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5352 | HTTPS FTP |
-Validation report
Summary document | emd_5352_validation.pdf.gz | 381.5 KB | Display | EMDB validaton report |
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Full document | emd_5352_full_validation.pdf.gz | 381 KB | Display | |
Data in XML | emd_5352_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5352 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5352 | HTTPS FTP |
-Related structure data
Related structure data | 2mmeM 3j0rMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5352.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an reconstruction of the type III secretion needle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 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 : Shigella needle
Entire | Name: Shigella needle |
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Components |
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-Supramolecule #1000: Shigella needle
Supramolecule | Name: Shigella needle / type: sample / ID: 1000 / Oligomeric state: helical assembly of MxiH / Number unique components: 1 |
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-Macromolecule #1: MxiH
Macromolecule | Name: MxiH / type: protein_or_peptide / ID: 1 / Name.synonym: MxiH / Recombinant expression: Yes / Database: NCBI |
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Source (natural) | Organism: Shigella flexneri (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.4 / Details: 20 mM Tris, pH 7.4, 150 mM NaCl, 2mM MgSO4 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 3.5 seconds before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Temperature | Min: 50 K / Max: 60 K / Average: 50 K |
Specialist optics | Energy filter - Name: JEOL Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 10.0 eV |
Date | Jul 2, 2008 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 330 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 89285 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.6 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: top entry / Specimen holder model: OTHER |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.30 Å Applied symmetry - Helical parameters - Δ&Phi: 64.06 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER |
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CTF correction | Details: CTFFIND3 Each particle |