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Yorodumi- PDB-7k08: Cryo-EM structure of the nonameric EscV cytosolic domain from the... -
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-Basic information
Entry | Database: PDB / ID: 7k08 | ||||||||||||
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Title | Cryo-EM structure of the nonameric EscV cytosolic domain from the type III secretion system | ||||||||||||
Components | Translocator EscV | ||||||||||||
Keywords | PROTEIN TRANSPORT / Injectisome / Nonamer / Export Apparatus / Secretion | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Escherichia coli O127:H6 (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||||||||
Authors | Majewski, D.D. / Lyons, B.J.E. / Atkinson, C.E. / Strynadka, N.C.J. | ||||||||||||
Funding support | Canada, 3items
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Citation | Journal: J Struct Biol / Year: 2020 Title: Cryo-EM analysis of the SctV cytosolic domain from the enteropathogenic E. coli T3SS injectisome. Authors: Dorothy D Majewski / Bronwyn J E Lyons / Claire E Atkinson / Natalie C J Strynadka / Abstract: The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, ...The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, through which signal-modulating effector proteins are secreted. The inner membrane pore protein SctV controls the hierarchy of substrate selection and may also be involved in energizing secretion. We present the 4.7 Å cryo-EM structure of the SctV cytosolic domain (SctV) from the enteropathogenic Escherichia coli injectisome. SctV forms a nonameric ring with primarily electrostatic interactions between its subunits. Molecular dynamics simulations show that monomeric SctV maintains a closed conformation, in contrast with previous studies on flagellar homologue FlhA. Comparison with substrate-bound homologues suggest that a conformational change would be required to accommodate binding partners. | ||||||||||||
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 | 7k08.cif.gz | 1000.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7k08.ent.gz | 832.9 KB | Display | PDB format |
PDBx/mmJSON format | 7k08.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7k08_validation.pdf.gz | 843.7 KB | Display | wwPDB validaton report |
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Full document | 7k08_full_validation.pdf.gz | 894.6 KB | Display | |
Data in XML | 7k08_validation.xml.gz | 88.8 KB | Display | |
Data in CIF | 7k08_validation.cif.gz | 118.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/7k08 ftp://data.pdbj.org/pub/pdb/validation_reports/k0/7k08 | HTTPS FTP |
-Related structure data
Related structure data | 22589MC 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: 39081.633 Da / Num. of mol.: 9 / Fragment: cytosolic domain (UNP residues 338-675) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria) Strain: E2348/69 / EPEC / Gene: escV, E2348C_3949 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UMA7 |
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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: EscV Cytosolic Nonamer Ring / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.35 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||
Symmetry | Point symmetry: C9 (9 fold cyclic) | ||||||||||||||||||
3D reconstruction | Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83566 / Symmetry type: POINT |