4O9Y | pdb_00004o9y

Crystal Structure of TcdA1

• PDB DOI: https://doi.org/10.2210/pdb4O9Y/pdb
• Entry: 4O9Y supersedes: 1VW1, 1VW2

• Classification: TOXIN
• Organism(s): Photorhabdus luminescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-03 Released: 2014-02-26 
• Deposition Author(s): Meusch, D., Gatsogiannis, C., Efremov, R.G., Lang, A.E., Hofnagel, O., Vetter, I.R., Aktories, K., Raunser, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.295 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Literature

Mechanism of Tc toxin action revealed in molecular detail.

Meusch, D., Gatsogiannis, C., Efremov, R.G., Lang, A.E., Hofnagel, O., Vetter, I.R., Aktories, K., Raunser, S.

(2014) Nature 508: 61-65

• PubMed: 24572368 
• DOI: https://doi.org/10.1038/nature13015
• Primary Citation Related Structures: 
  4O9X, 4O9Y


• PubMed 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 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.

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Organizational Affiliation: 
• 1] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany [2].
Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.
1] Institut für Experimentelle und Klinische Pharmakologie und Toxikologie, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.
1] Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany [2] Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 2,832.29 kDa 
• Atom Count: 197,663 
• Modeled Residue Count: 24,898 
• Deposited Residue Count: 25,160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TcdA1	A, B, C, D, E, F, G, H, I, J	2,516	Photorhabdus luminescens	Mutation(s): 0  Gene Names: tcdA, tcdA1
UniProt
Find proteins for Q9RN43 (Photorhabdus luminescens) Explore Q9RN43  Go to UniProtKB:  Q9RN43

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.295 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 303.25	α = 90
b = 320.73	β = 90
c = 667.62	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-26 
Deposition Author(s): Meusch, D., Gatsogiannis, C., Efremov, R.G., Lang, A.E., Hofnagel, O., Vetter, I.R., Aktories, K., Raunser, S.
• This entry supersedes: 1VW1, 1VW2

Revision History  

• Version 1.0: 2014-02-26
  Type: Initial release
  
• Version 1.1: 2014-03-05
  Changes: Other
• Version 1.2: 2014-07-09
  Changes: Other
• Version 1.3: 2014-12-10
  Changes: Other
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references