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Yorodumi- EMDB-20046: Structure of Salmonella type III secretion system needle filament -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20046 | |||||||||
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Title | Structure of Salmonella type III secretion system needle filament | |||||||||
Map data | PrgI needle attached to base | |||||||||
Sample |
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Keywords | type III secretion system / salmonella / helical reconstruction / PROTEIN TRANSPORT | |||||||||
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 | Salmonella typhimurium (strain SL1344) (bacteria) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Guo EZ / Galan JE | |||||||||
Funding support | United States, 1 items
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Citation | Journal: PLoS Biol / Year: 2019 Title: A polymorphic helix of a Salmonella needle protein relays signals defining distinct steps in type III secretion. Authors: Emily Z Guo / Daniel C Desrosiers / Jan Zalesak / James Tolchard / Mélanie Berbon / Birgit Habenstein / Thomas Marlovits / Antoine Loquet / Jorge E Galán / Abstract: Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines ...Type III protein-secretion machines are essential for the interactions of many pathogenic or symbiotic bacterial species with their respective eukaryotic hosts. The core component of these machines is the injectisome, a multiprotein complex that mediates the selection of substrates, their passage through the bacterial envelope, and ultimately their delivery into eukaryotic target cells. The injectisome is composed of a large cytoplasmic complex or sorting platform, a multiring base embedded in the bacterial envelope, and a needle-like filament that protrudes several nanometers from the bacterial surface and is capped at its distal end by the tip complex. A characteristic feature of these machines is that their activity is stimulated by contact with target host cells. The sensing of target cells, thought to be mediated by the distal tip of the needle filament, generates an activating signal that must be transduced to the secretion machine by the needle filament. Here, through a multidisciplinary approach, including solid-state NMR (SSNMR) and cryo electron microscopy (cryo-EM) analyses, we have identified critical residues of the needle filament protein of a Salmonella Typhimurium type III secretion system that are involved in the regulation of the activity of the secretion machine. We found that mutations in the needle filament protein result in various specific phenotypes associated with different steps in the type III secretion process. More specifically, these studies reveal an important role for a polymorphic helix of the needle filament protein and the residues that line the lumen of its central channel in the control of type III secretion. | |||||||||
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_20046.map.gz | 1 MB | EMDB map data format | |
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Header (meta data) | emd-20046-v30.xml emd-20046.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_20046.png | 161.4 KB | ||
Filedesc metadata | emd-20046.cif.gz | 5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20046 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20046 | HTTPS FTP |
-Validation report
Summary document | emd_20046_validation.pdf.gz | 463.7 KB | Display | EMDB validaton report |
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Full document | emd_20046_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | emd_20046_validation.xml.gz | 5.1 KB | Display | |
Data in CIF | emd_20046_validation.cif.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20046 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20046 | HTTPS FTP |
-Related structure data
Related structure data | 6ofhMC 6ofeC 6offC 6ofgC 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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-Map
File | Download / File: emd_20046.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PrgI needle attached to base | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.708 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 : filament structure of PrgI needle attached to the base
Entire | Name: filament structure of PrgI needle attached to the base |
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Components |
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-Supramolecule #1: filament structure of PrgI needle attached to the base
Supramolecule | Name: filament structure of PrgI needle attached to the base type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Salmonella typhimurium (strain SL1344) (bacteria) |
-Macromolecule #1: Protein PrgI
Macromolecule | Name: Protein PrgI / type: protein_or_peptide / ID: 1 / Number of copies: 19 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella typhimurium (strain SL1344) (bacteria) / Strain: SL1344 |
Molecular weight | Theoretical: 8.864868 KDa |
Sequence | String: MATPWSGYLD DVSAKFDTGV DNLQTQVTEA LDKLAAKPSD PALLAAYQSK LSEYNLYRNA QSNTVKVFKD IDAAIIQNFR UniProtKB: Type III secretion system apparatus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 4.24 Å Applied symmetry - Helical parameters - Δ&Phi: 63.35 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53866 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE |