+Open data
-Basic information
Entry | Database: PDB / ID: 5lki | |||||||||
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Title | Cryo-EM structure of the Tc toxin TcdA1 in its pore state | |||||||||
Components | TcdA1 | |||||||||
Keywords | TOXIN / nanodisc / injection / pore-forming | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Photorhabdus luminescens (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å | |||||||||
Authors | Gatsogiannis, C. / Merino, F. / Prumbaum, D. / Roderer, D. / Leidreiter, F. / Meusch, D. / Raunser, S. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Nat Struct Mol Biol / Year: 2016 Title: Membrane insertion of a Tc toxin in near-atomic detail. Authors: Christos Gatsogiannis / Felipe Merino / Daniel Prumbaum / Daniel Roderer / Franziska Leidreiter / Dominic Meusch / Stefan Raunser / Abstract: Tc toxins from pathogenic bacteria use a special syringe-like mechanism to perforate the host cell membrane and inject a deadly enzyme into the host cytosol. The molecular mechanism of this unusual ...Tc toxins from pathogenic bacteria use a special syringe-like mechanism to perforate the host cell membrane and inject a deadly enzyme into the host cytosol. The molecular mechanism of this unusual injection system is poorly understood. Using electron cryomicroscopy, we determined the structure of TcdA1 from Photorhabdus luminescens embedded in lipid nanodiscs. In our structure, compared with the previous structure of TcdA1 in the prepore state, the transmembrane helices rearrange in the membrane and open the initially closed pore. However, the helices do not span the complete membrane; instead, the loops connecting the helices form the rim of the funnel. Lipid head groups reach into the space between the loops and consequently stabilize the pore conformation. The linker domain is folded and packed into a pocket formed by the other domains of the toxin, thereby considerably contributing to stabilization of the pore state. | |||||||||
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 | 5lki.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5lki.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5lki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lki_validation.pdf.gz | 899.4 KB | Display | wwPDB validaton report |
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Full document | 5lki_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5lki_validation.xml.gz | 229.9 KB | Display | |
Data in CIF | 5lki_validation.cif.gz | 333.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/5lki ftp://data.pdbj.org/pub/pdb/validation_reports/lk/5lki | HTTPS FTP |
-Related structure data
Related structure data | 4068MC 5lkhC 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: 283229.406 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus luminescens (bacteria) / Gene: tcdA, tcdA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RN43 |
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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: Structure of TcdA1 in pore state, determined in lipid nanodisc Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||
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Molecular weight | Value: 1.4 MDa / Experimental value: NO | ||||||||||||
Source (natural) | Organism: Photorhabdus luminescens (bacteria) | ||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) / Plasmid: pET-19b | ||||||||||||
Buffer solution | pH: 11 | ||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/1 | ||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Details: Cs corrected microscope |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 15.4 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 1957 |
Image scans | Movie frames/image: 7 |
-Processing
Software | Name: PHENIX / Version: 1.10_2152: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 30061 / Details: particles were picked manually | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C5 (5 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13000 Details: The density was filtered to its local resolution, using localfilt (SPARX) and RESMAP Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.46 Å | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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