+Open data
-Basic information
Entry | Database: PDB / ID: 6ogd | |||||||||||||||
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Title | Cryo-EM structure of YenTcA in its prepore state | |||||||||||||||
Components |
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Keywords | TOXIN / Membrane protein Pore-forming toxin Complex | |||||||||||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / : / polysaccharide catabolic process / extracellular region Similarity search - Function | |||||||||||||||
Biological species | Yersinia entomophaga (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | |||||||||||||||
Authors | Piper, S.J. / Brillault, L. / Box, J.K. / Landsberg, M.J. | |||||||||||||||
Funding support | Australia, New Zealand, 4items
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Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin. Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren ...Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren Hartley-Tassell / Thomas Ve / Jason N Busby / Julie E Dalziel / J Shaun Lott / Ben Hankamer / Henning Stahlberg / Mark R H Hurst / Michael J Landsberg / Abstract: ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen ...ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen Yersinia entomophaga. Here we present cryo-EM structures of YenTcA, purified from the native source. The soluble pre-pore structure, determined at an average resolution of 4.4 Å, reveals a pentameric assembly that in contrast to other characterised ABC toxins is formed by two TcA-like proteins (YenA1 and YenA2) and decorated by two endochitinases (Chi1 and Chi2). We also identify conformational changes that accompany membrane pore formation by visualising YenTcA inserted into liposomes. A clear outward rotation of the Chi1 subunits allows for access of the protruding translocation pore to the membrane. Our results highlight structural and functional diversity within the ABC toxin subfamily, explaining how different ABC toxins are capable of recognising diverse hosts. | |||||||||||||||
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 | 6ogd.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6ogd.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 6ogd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ogd_validation.pdf.gz | 963.3 KB | Display | wwPDB validaton report |
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Full document | 6ogd_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ogd_validation.xml.gz | 277.4 KB | Display | |
Data in CIF | 6ogd_validation.cif.gz | 431.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/6ogd ftp://data.pdbj.org/pub/pdb/validation_reports/og/6ogd | HTTPS FTP |
-Related structure data
Related structure data | 20053MC 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: 129912.320 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A877 #2: Protein | Mass: 156324.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A878 #3: Protein | Mass: 69740.609 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Yersinia entomophaga (bacteria) / References: UniProt: B6A879, chitinase |
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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: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 2.08 MDa |
Source (natural) | Organism: Yersinia entomophaga (bacteria) / Strain: MH96 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | 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: 80 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 19713 | ||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9856 / Symmetry type: POINT |