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Yorodumi- EMDB-1416: Helical structure of the needle of the type III secretion system ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1416 | |||||||||
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Title | Helical structure of the needle of the type III secretion system of Shigella flexneri. | |||||||||
Map data | ccp4 map of reconstruction of Shigella flexneri T3SS needle | |||||||||
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 / cell surface / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Shigella flexneri (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / negative staining / Resolution: 16.0 Å | |||||||||
Authors | Cordes FS / Komoriya K / Larquet E / Yang S / Egelman EH / Blocker A / Lea SM | |||||||||
Citation | Journal: J Biol Chem / Year: 2003 Title: Helical structure of the needle of the type III secretion system of Shigella flexneri. Authors: Frank S Cordes / Kaoru Komoriya / Eric Larquet / Shixin Yang / Edward H Egelman / Ariel Blocker / Susan M Lea / Abstract: Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS- ...Gram-negative bacteria commonly interact with animal and plant hosts using type III secretion systems (TTSSs) for translocation of proteins into eukaryotic cells during infection. 10 of the 25 TTSS-encoding genes are homologous to components of the bacterial flagellar basal body, which the TTSS needle complex morphologically resembles. This indicates a common ancestry, although no TTSS sequence homologues for the genes encoding the flagellum are found. We here present an approximately 16-A structure of the central component, the needle, of the TTSS. Although the needle subunit is significantly smaller and shares no sequence homology with the flagellar hook and filament, it shares a common helical architecture ( approximately 5.6 subunits/turn, 24-A helical pitch). This common architecture implies that there will be further mechanistic analogies in the functioning of these two bacterial systems. | |||||||||
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_1416.map.gz | 281.1 KB | EMDB map data format | |
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Header (meta data) | emd-1416-v30.xml emd-1416.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | 1416.gif | 10.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1416 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1416 | HTTPS FTP |
-Validation report
Summary document | emd_1416_validation.pdf.gz | 197.2 KB | Display | EMDB validaton report |
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Full document | emd_1416_full_validation.pdf.gz | 196.3 KB | Display | |
Data in XML | emd_1416_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1416 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1416 | HTTPS FTP |
-Related structure data
Related structure data | 2v6lM 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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-Map
File | Download / File: emd_1416.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ccp4 map of reconstruction of Shigella flexneri T3SS needle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.65 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 flexneri T3SS needle - MxiH polymer
Entire | Name: Shigella flexneri T3SS needle - MxiH polymer |
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Components |
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-Supramolecule #1000: Shigella flexneri T3SS needle - MxiH polymer
Supramolecule | Name: Shigella flexneri T3SS needle - MxiH polymer / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 1 |
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-Macromolecule #1: MxiH
Macromolecule | Name: MxiH / type: protein_or_peptide / ID: 1 / Name.synonym: MxiH / Oligomeric state: helical polymer / Recombinant expression: Yes |
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Source (natural) | Organism: Shigella flexneri (bacteria) / Strain: M90T / Location in cell: extracellular |
Molecular weight | Experimental: 9265 MDa |
Recombinant expression | Organism: Shigella flexneri (bacteria) / Recombinant plasmid: pKT001 |
Sequence | InterPro: Type III secretion system, needle protein |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 / Details: 10mM Tris pH 7.5 |
Staining | Type: NEGATIVE / Details: 2% uranyl acetate, pH 7.5 |
Grid | Details: 200 mesh carbon coated copper |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI/PHILIPS CM120T |
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Temperature | Average: 293 K |
Details | low dose conditions |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 18 / Average electron dose: 10 e/Å2 / Details: 1600dpi, 2.65 Angstrom per pixel |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 0.7 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
-Image processing
Details | the 5-start helix is left handed |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: OTHER / Software - Name: SPIDER and MRC / Details: see paper |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: BUSTER-TnT |
Details | Protocol: Rigid Body. Fitted by hand and optimised using URO. Helical parameters used. |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 50 / Target criteria: Correlation Coefficient and R_factor |
Output model | PDB-2v6l: |