3C0O

Crystal structure of the proaerolysin mutant Y221G complexed with mannose-6-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.

Degiacomi, M.T.Iacovache, I.Pernot, L.Chami, M.Kudryashev, M.Stahlberg, H.van der Goot, F.G.Dal Peraro, M.

(2013) Nat.Chem.Biol. 9: 623-629

  • DOI: 10.1038/nchembio.1312
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Aerolysin is the founding member of a superfamily of β-pore-forming toxins whose pore structure is unknown. We have combined X-ray crystallography, cryo-EM, molecular dynamics and computational modeling to determine the structures of aerolysin mutant ...

    Aerolysin is the founding member of a superfamily of β-pore-forming toxins whose pore structure is unknown. We have combined X-ray crystallography, cryo-EM, molecular dynamics and computational modeling to determine the structures of aerolysin mutants in their monomeric and heptameric forms, trapped at various stages of the pore formation process. A dynamic modeling approach based on swarm intelligence was applied, whereby the intrinsic flexibility of aerolysin extracted from new X-ray structures was used to fully exploit the cryo-EM spatial restraints. Using this integrated strategy, we obtained a radically new arrangement of the prepore conformation and a near-atomistic structure of the aerolysin pore, which is fully consistent with all of the biochemical data available so far. Upon transition from the prepore to pore, the aerolysin heptamer shows a unique concerted swirling movement, accompanied by a vertical collapse of the complex, ultimately leading to the insertion of a transmembrane β-barrel.


    Related Citations: 
    • Crystallization of a proform of aerolysin, a hole-forming toxin from Aeromonas hydrophila.
      Tucker, A.D.,Parker, M.W.,Tsernoglou, D.,Buckley, J.T.
      (1990) J.Mol.Biol. 212: 561
    • Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states.
      Parker, M.W.,Buckley, J.T.,Postma, J.P.,Tucker, A.D.,Leonard, K.,Pattus, F.,Tsernoglou, D.
      (1994) Nature 367: 292


    Organizational Affiliation

    1] Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland. [2] [3].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aerolysin
A, B
470Aeromonas hydrophilaMutation(s): 1 
Gene Names: aerA
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Adventitious Membrane Proteins: Beta-sheet Pore-forming Toxins/Attack Complexes
Protein: 
Aerolysin pore-forming toxin Y221G mutant
Find proteins for P09167 (Aeromonas hydrophila)
Go to UniProtKB:  P09167
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M6P
Query on M6P

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE-6-PHOSPHATE
C6 H13 O9 P
NBSCHQHZLSJFNQ-PQMKYFCFSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.954α = 90.00
b = 90.780β = 90.00
c = 165.805γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-10-02
    Type: Database references