3C0O

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3C0M, 3C0N, 3C0O

  • 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 mutants in their monomeric and heptameric forms, trapped at various stages of the pore formation process ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AerolysinA, B470Aeromonas hydrophilaMutation(s): 1 
Gene Names: aerA
Membrane Entity: Yes 
UniProt
Find proteins for P09167 (Aeromonas hydrophila)
Explore P09167 
Go to UniProtKB:  P09167
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M6P (Subject of Investigation/LOI)
Query on M6P

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]6-O-phosphono-alpha-D-mannopyranose
C6 H13 O9 P
NBSCHQHZLSJFNQ-PQMKYFCFSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.954α = 90
b = 90.78β = 90
c = 165.805γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-02
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary