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Yorodumi- PDB-6s3l: Structure of the core of the flagellar export apparatus from Vibr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s3l | ||||||||||||||||||
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Title | Structure of the core of the flagellar export apparatus from Vibrio mimicus, the FliPQR-FlhB complex. | ||||||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / flagella / T3SS / export apparatus / export gate | ||||||||||||||||||
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 | Vibrio mimicus CAIM 602 (bacteria) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||||||||
Authors | Kuhlen, L. / Johnson, S. / Deme, J.C. / Lea, S.M. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Nat Commun / Year: 2020 Title: The substrate specificity switch FlhB assembles onto the export gate to regulate type three secretion. Authors: Lucas Kuhlen / Steven Johnson / Andreas Zeitler / Sandra Bäurle / Justin C Deme / Joseph J E Caesar / Rebecca Debo / Joseph Fisher / Samuel Wagner / Susan M Lea / Abstract: Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins ...Protein secretion through type-three secretion systems (T3SS) is critical for motility and virulence of many bacteria. Proteins are transported through an export gate containing three proteins (FliPQR in flagella, SctRST in virulence systems). A fourth essential T3SS protein (FlhB/SctU) functions to "switch" secretion substrate specificity once the growing hook/needle reach their determined length. Here, we present the cryo-electron microscopy structure of an export gate containing the switch protein from a Vibrio flagellar system at 3.2 Å resolution. The structure reveals that FlhB/SctU extends the helical export gate with its four predicted transmembrane helices wrapped around FliPQR/SctRST. The unusual topology of the FlhB/SctU helices creates a loop wrapped around the bottom of the closed export gate. Structure-informed mutagenesis suggests that this loop is critical in gating secretion and we propose that a series of conformational changes in the T3SS trigger opening of the gate through interactions between FlhB/SctU and FliPQR/SctRST. | ||||||||||||||||||
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 | 6s3l.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s3l.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 6s3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6s3l_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6s3l_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6s3l_validation.xml.gz | 62.1 KB | Display | |
Data in CIF | 6s3l_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/6s3l ftp://data.pdbj.org/pub/pdb/validation_reports/s3/6s3l | HTTPS FTP |
-Related structure data
Related structure data | 10093MC 6s3rC 6s3sC 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: 32431.307 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio mimicus CAIM 602 (bacteria) / Gene: fliP, AL544_009685 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2J9UXT5 #2: Protein | | Mass: 28764.324 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio mimicus CAIM 602 (bacteria) / Gene: AL544_009675 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8S9I5 #3: Protein | Mass: 10333.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio mimicus CAIM 602 (bacteria) / Gene: fliQ, AL544_009680 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8S9F5 #4: Protein | | Mass: 46265.730 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio mimicus CAIM 602 (bacteria) / Gene: flhB, AL544_009670 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1D8S9F8 |
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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: FliPQR-FlhB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||
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Molecular weight | Value: 0.26 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Vibrio mimicus CAIM 602 (bacteria) | |||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21 (bacteria) | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K / Details: 10 seconds wait time |
-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 / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1386230 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162408 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.2 Å Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Refine LS restraints |
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