+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2552 | |||||||||
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Title | Electron cryo-microscopy of TcdA1 in pore state. | |||||||||
Map data | Reconstruction of TcdA1 in pore state | |||||||||
Sample |
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Keywords | Photorhabdus / Tc toxin / ABC toxin / translocation | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Photorhabdus luminescens (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.0 Å | |||||||||
Authors | Gatsogiannis C / Meusch D / Efremov RG / Lang AE / Hofnagel O / Vetter IR / Aktories K / Raunser S | |||||||||
Citation | Journal: Nature / Year: 2014 Title: Mechanism of Tc toxin action revealed in molecular detail. Authors: Dominic Meusch / Christos Gatsogiannis / Rouslan G Efremov / Alexander E Lang / Oliver Hofnagel / Ingrid R Vetter / Klaus Aktories / Stefan Raunser / Abstract: Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell, including in humans. The underlying mechanism is complex but poorly ...Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell, including in humans. The underlying mechanism is complex but poorly understood. Here we report the first, to our knowledge, high-resolution structures of a TcA subunit in its prepore and pore state and of a complete 1.7 megadalton Tc complex. The structures reveal that, in addition to a translocation channel, TcA forms four receptor-binding sites and a neuraminidase-like region, which are important for its host specificity. pH-induced opening of the shell releases an entropic spring that drives the injection of the TcA channel into the membrane. Binding of TcB/TcC to TcA opens a gate formed by a six-bladed β-propeller and results in a continuous protein translocation channel, whose architecture and properties suggest a novel mode of protein unfolding and translocation. Our results allow us to understand key steps of infections involving Tc toxins at the molecular level. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2552.map.gz | 5.8 MB | EMDB map data format | |
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Header (meta data) | emd-2552-v30.xml emd-2552.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_2552.png | 1.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2552 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2552 | HTTPS FTP |
-Validation report
Summary document | emd_2552_validation.pdf.gz | 203.7 KB | Display | EMDB validaton report |
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Full document | emd_2552_full_validation.pdf.gz | 202.8 KB | Display | |
Data in XML | emd_2552_validation.xml.gz | 5.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2552 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2552 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2552.map.gz / Format: CCP4 / Size: 39.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of TcdA1 in pore state | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : TcdA1
Entire | Name: TcdA1 |
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Components |
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-Supramolecule #1000: TcdA1
Supramolecule | Name: TcdA1 / type: sample / ID: 1000 / Oligomeric state: Pentamer / Number unique components: 1 |
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Molecular weight | Experimental: 1.41 MDa / Theoretical: 1.41 MDa |
-Macromolecule #1: TcdA1
Macromolecule | Name: TcdA1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Pentamer / Recombinant expression: Yes |
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Source (natural) | Organism: Photorhabdus luminescens (bacteria) |
Molecular weight | Experimental: 283 KDa / Theoretical: 283 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | UniProtKB: TcdA1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 11 Details: 50 mM CAPS,100 mM NaCl, 0.05% Tween-20, 5% glycerol |
Grid | Details: C-Flat 2/1-4C copper 400 mesh, with additional thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 1 sec before plunging |
-Electron microscopy
Microscope | JEOL 3200FSC |
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Specialist optics | Energy filter - Name: in-column Omega filter / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 15.0 eV |
Date | Aug 27, 2012 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 605 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 124472 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 0.0029 µm / Nominal defocus min: 0.0004 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL 3200FSC CRYOHOLDER |
-Image processing
CTF correction | Details: Each Particle |
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Final reconstruction | Applied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Sparx / Number images used: 13303 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: DireX |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |