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Yorodumi- PDB-7k7k: Structure of the EPEC type III secretion injectisome EspA filament -
+Open data
-Basic information
Entry | Database: PDB / ID: 7k7k | |||||||||
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Title | Structure of the EPEC type III secretion injectisome EspA filament | |||||||||
Components | Translocon EspA | |||||||||
Keywords | PROTEIN TRANSPORT / Transport / filament / secretion system | |||||||||
Function / homology | EspA-like secreted protein / EspA-like secreted protein / EspA/CesA-like / Translocon EspA Function and homology information | |||||||||
Biological species | Escherichia coli O127:H6 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Lyons, B.J.E. / Atkinson, C.E. / Strynadka, N.C.J. | |||||||||
Funding support | Canada, 2items
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Citation | Journal: Structure / Year: 2021 Title: Cryo-EM structure of the EspA filament from enteropathogenic Escherichia coli: Revealing the mechanism of effector translocation in the T3SS. Authors: Bronwyn J E Lyons / Claire E Atkinson / Wanyin Deng / Antonio Serapio-Palacios / B Brett Finlay / Natalie C J Strynadka / Abstract: The type III secretion system (T3SS) is a virulence mechanism employed by Gram-negative pathogens. The T3SS forms a proteinaceous channel that projects a needle into the extracellular medium where it ...The type III secretion system (T3SS) is a virulence mechanism employed by Gram-negative pathogens. The T3SS forms a proteinaceous channel that projects a needle into the extracellular medium where it interacts with the host cell to deliver virulence factors. Enteropathogenic Escherichia coli (EPEC) is unique in adopting a needle extension to the T3SS-a filament formed by EspA-which is absolutely required for efficient colonization of the gut. Here, we describe the cryoelectron microscopy structure of native EspA filaments from EPEC at 3.6-Å resolution. Within the filament, positively charged residues adjacent to a hydrophobic groove line the lumen of the filament in a spiral manner, suggesting a mechanism of substrate translocation mediated via electrostatics. Using structure-guided mutagenesis, in vivo studies corroborate the role of these residues in secretion and translocation function. The high-resolution structure of the EspA filament could aid in structure-guided drug design of antivirulence therapeutics. | |||||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 7k7k.cif.gz | 760.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k7k.ent.gz | 650.3 KB | Display | PDB format |
PDBx/mmJSON format | 7k7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k7k_validation.pdf.gz | 796.3 KB | Display | wwPDB validaton report |
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Full document | 7k7k_full_validation.pdf.gz | 803.1 KB | Display | |
Data in XML | 7k7k_validation.xml.gz | 107.4 KB | Display | |
Data in CIF | 7k7k_validation.cif.gz | 147.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/7k7k ftp://data.pdbj.org/pub/pdb/validation_reports/k7/7k7k | HTTPS FTP |
-Related structure data
Related structure data | 22701MC 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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-Components
#1: Protein | Mass: 20482.811 Da / Num. of mol.: 28 / Source method: isolated from a natural source Source: (natural) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / References: UniProt: B7UM94 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: EspA filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Escherichia coli O127:H6 str. E2348/69 (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: 0.475 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software | Name: RELION / Version: 3 / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Helical symmerty | Angular rotation/subunit: 64.3 ° / Axial rise/subunit: 4.4 Å / Axial symmetry: C1 |
3D reconstruction | Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15523 / Symmetry type: HELICAL |