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Yorodumi- PDB-6f2d: A FliPQR complex forms the core of the Salmonella type III secret... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f2d | |||||||||||||||
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Title | A FliPQR complex forms the core of the Salmonella type III secretion system export apparatus. | |||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / T3SS / Flagella / Cryo-EM / Export / Membrane protein | |||||||||||||||
Function / homology | Function and homology information bacterial-type flagellum organization / bacterial-type flagellum basal body / bacterial-type flagellum assembly / protein secretion / protein targeting / membrane => GO:0016020 / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Salmonella enterica subsp. enterica (bacteria) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||
Authors | Johnson, S. / Kuhlen, L. / Abrusci, P. / Lea, S.M. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nat Struct Mol Biol / Year: 2018 Title: Structure of the core of the type III secretion system export apparatus. Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / ...Authors: Lucas Kuhlen / Patrizia Abrusci / Steven Johnson / Joseph Gault / Justin Deme / Joseph Caesar / Tobias Dietsche / Mehari Tesfazgi Mebrhatu / Tariq Ganief / Boris Macek / Samuel Wagner / Carol V Robinson / Susan M Lea / Abstract: Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are ...Export of proteins through type III secretion systems is critical for motility and virulence of many major bacterial pathogens. Three putative integral membrane proteins (FliP, FliQ, FliR) are suggested to form the core of an export gate in the inner membrane, but their structure, assembly and location within the final nanomachine remain unclear. Here, we present the cryoelectron microscopy structure of the Salmonella Typhimurium FliP-FliQ-FliR complex at 4.2 Å. None of the subunits adopt canonical integral membrane protein topologies, and common helix-turn-helix structural elements allow them to form a helical assembly with 5:4:1 stoichiometry. Fitting of the structure into reconstructions of intact secretion systems, combined with cross-linking, localize the export gate as a core component of the periplasmic portion of the machinery. This study thereby identifies the export gate as a key element of the secretion channel and implies that it primes the helical architecture of the components assembling downstream. | |||||||||||||||
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 | 6f2d.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f2d.ent.gz | 219.9 KB | Display | PDB format |
PDBx/mmJSON format | 6f2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/6f2d ftp://data.pdbj.org/pub/pdb/validation_reports/f2/6f2d | HTTPS FTP |
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-Related structure data
Related structure data | 4173MC 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: 26769.021 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica (bacteria) Gene: fliP, LTSERUB_0568 / Production host: Escherichia coli (E. coli) / Strain (production host): Mt56 / References: UniProt: G5QE81, UniProt: P54700*PLUS #2: Protein | | Mass: 33069.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 265 onwards constitute the Twin-Strep tag used for purification Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: fliR, flaP, STM1981 / Production host: Escherichia coli (E. coli) / Strain (production host): Mt56 / References: UniProt: P54702 #3: Protein | Mass: 9606.758 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: fliQ, flaQ, STY2188, t0897 / Production host: Escherichia coli (E. coli) / Strain (production host): Mt56 / References: UniProt: P0A1L6, UniProt: P0A1L5*PLUS |
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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 flagellar type III secretion system export apparatus components FliP, FliQ and FliRType three secretion system Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 195 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Salmonella enterica (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) / Strain: Mt56 |
Buffer solution | pH: 8 |
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: SPOT SCAN | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording |
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-Processing
Software | Name: PHENIX / Version: 1.10_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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Image processing | Details: Images from K2 were also added. | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97718 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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