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Yorodumi- PDB-5tcq: Near-atomic resolution cryo-EM structure of the Salmonella SPI-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5tcq | ||||||
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Title | Near-atomic resolution cryo-EM structure of the Salmonella SPI-1 type III secretion injectisome secretin InvG | ||||||
Components | Protein InvG | ||||||
Keywords | MEMBRANE PROTEIN / Bacterial / secretion / injectisome | ||||||
Function / homology | Function and homology information type III protein secretion system complex / type II protein secretion system complex / protein secretion by the type III secretion system / protein secretion / cell outer membrane / identical protein binding Similarity search - Function | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Worrall, L.J. / Hong, C. / Vuckovic, M. / Bergeron, J.R.C. / Huang, R.K. / Yu, Z. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nature / Year: 2016 Title: Near-atomic-resolution cryo-EM analysis of the Salmonella T3S injectisome basal body. Authors: L J Worrall / C Hong / M Vuckovic / W Deng / J R C Bergeron / D D Majewski / R K Huang / T Spreter / B B Finlay / Z Yu / N C J Strynadka / Abstract: The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, ...The type III secretion (T3S) injectisome is a specialized protein nanomachine that is critical for the pathogenicity of many Gram-negative bacteria, including purveyors of plague, typhoid fever, whooping cough, sexually transmitted infections and major nosocomial infections. This syringe-shaped 3.5-MDa macromolecular assembly spans both bacterial membranes and that of the infected host cell. The internal channel formed by the injectisome allows for the direct delivery of partially unfolded virulence effectors into the host cytoplasm. The structural foundation of the injectisome is the basal body, a molecular lock-nut structure composed predominantly of three proteins that form highly oligomerized concentric rings spanning the inner and outer membranes. Here we present the structure of the prototypical Salmonella enterica serovar Typhimurium pathogenicity island 1 basal body, determined using single-particle cryo-electron microscopy, with the inner-membrane-ring and outer-membrane-ring oligomers defined at 4.3 Å and 3.6 Å resolution, respectively. This work presents the first, to our knowledge, high-resolution structural characterization of the major components of the basal body in the assembled state, including that of the widespread class of outer-membrane portals known as secretins. | ||||||
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 | 5tcq.cif.gz | 861.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tcq.ent.gz | 683.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tcq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5tcq_validation.pdf.gz | 947.2 KB | Display | wwPDB validaton report |
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Full document | 5tcq_full_validation.pdf.gz | 964 KB | Display | |
Data in XML | 5tcq_validation.xml.gz | 115.6 KB | Display | |
Data in CIF | 5tcq_validation.cif.gz | 160.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/5tcq ftp://data.pdbj.org/pub/pdb/validation_reports/tc/5tcq | HTTPS FTP |
-Related structure data
Related structure data | 8399MC 8398C 8400C 8401C 5tcpC 5tcrC 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: 61835.559 Da / Num. of mol.: 15 / Source method: isolated from a natural source Source: (natural) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) References: UniProt: P35672 |
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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: Type III injectisome basal body / Type: COMPLEX / Details: PrgH130-392 mutant / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 2 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 K |
-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 / Nominal magnification: 64000 X / Calibrated magnification: 29240 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Calibrated defocus min: 1300 nm / Calibrated defocus max: 3200 nm / Cs: 0.01 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 30 mradians |
Image recording | Average exposure time: 0.375 sec. / Electron dose: 1.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2685 |
EM imaging optics | Energyfilter name: Gatan GIF / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV |
Image scans | Sampling size: 5 µm / Width: 7676 / Height: 7420 / Movie frames/image: 48 / Used frames/image: 1-48 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 164300 | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C15 (15 fold cyclic) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83900 / Algorithm: FOURIER SPACE / Symmetry type: POINT | |||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL Details: Initial fitting was carried out with Chimera, followed by rebuilding and refinement in Rosetta, Phenix, and Coot. |