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Yorodumi- PDB-6duz: Structure of the periplasmic domains of PrgH and PrgK from the as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6duz | |||||||||
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Title | Structure of the periplasmic domains of PrgH and PrgK from the assembled Salmonella type III secretion injectisome needle complex | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Type III secretion system | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Hu, J. / Worrall, L.J. / Vuckovic, M. / Atkinson, C.E. / Strynadka, N.C.J. | |||||||||
Funding support | Canada, United States, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM analysis of the T3S injectisome reveals the structure of the needle and open secretin. Authors: J Hu / L J Worrall / C Hong / M Vuckovic / C E Atkinson / N Caveney / Z Yu / N C J Strynadka / Abstract: The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome ...The bacterial type III secretion system, or injectisome, is a syringe shaped nanomachine essential for the virulence of many disease causing Gram-negative bacteria. At the core of the injectisome structure is the needle complex, a continuous channel formed by the highly oligomerized inner and outer membrane hollow rings and a polymerized helical needle filament which spans through and projects into the infected host cell. Here we present the near-atomic resolution structure of a needle complex from the prototypical Salmonella Typhimurium SPI-1 type III secretion system, with local masking protocols allowing for model building and refinement of the major membrane spanning components of the needle complex base in addition to an isolated needle filament. This work provides significant insight into injectisome structure and assembly and importantly captures the molecular basis for substrate induced gating in the giant outer membrane secretin portal family. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6duz.cif.gz | 1.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6duz.ent.gz | 1.2 MB | Display | PDB format |
PDBx/mmJSON format | 6duz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6duz_validation.pdf.gz | 936.5 KB | Display | wwPDB validaton report |
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Full document | 6duz_full_validation.pdf.gz | 966.5 KB | Display | |
Data in XML | 6duz_validation.xml.gz | 198.9 KB | Display | |
Data in CIF | 6duz_validation.cif.gz | 275.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/6duz ftp://data.pdbj.org/pub/pdb/validation_reports/du/6duz | HTTPS FTP |
-Related structure data
Related structure data | 8913MC 8914C 8915C 8924C 6dv3C 6dv6C 6dwbC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 44509.367 Da / Num. of mol.: 24 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) References: UniProt: P41783 #2: Protein | Mass: 28245.287 Da / Num. of mol.: 24 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) References: UniProt: P41786 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of the periplasmic domains of PrgH and PrgK from the Salmonella SPI-1 type III secretion injectisome needle complex Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 80000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C24 (24 fold cyclic) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58000 / Symmetry type: POINT |