5EC5

Crystal structure of lysenin pore

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly.

Podobnik, M., Savory, P., Rojko, N., Kisovec, M., Wood, N., Hambley, R., Pugh, J., Wallace, E.J., McNeill, L., Bruce, M., Liko, I., Allison, T.M., Mehmood, S., Yilmaz, N., Kobayashi, T., Gilbert, R.J., Robinson, C.V., Jayasinghe, L., Anderluh, G.

(2016) Nat Commun 7: 11598-11598

  • DOI: 10.1038/ncomms11598

  • PubMed Abstract: 

    • The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly ...

    The invertebrate cytolysin lysenin is a member of the aerolysin family of pore-forming toxins that includes many representatives from pathogenic bacteria. Here we report the crystal structure of the lysenin pore and provide insights into its assembly mechanism. The lysenin pore is assembled from nine monomers via dramatic reorganization of almost half of the monomeric subunit structure leading to a β-barrel pore ∼10 nm long and 1.6-2.5 nm wide. The lysenin pore is devoid of additional luminal compartments as commonly found in other toxin pores. Mutagenic analysis and atomic force microscopy imaging, together with these structural insights, suggest a mechanism for pore assembly for lysenin. These insights are relevant to the understanding of pore formation by other aerolysin-like pore-forming toxins, which often represent crucial virulence factors in bacteria.

    Organizational Affiliation: 

    Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysenin
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S
298Eisenia fetidaMutations: K86E, Q85E, Q93E, G127D, S98E
Find proteins for O18423 (Eisenia fetida)
Go to UniProtKB:  O18423
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, K, L, M, O, P, R, S
MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
 Ligand Interaction
HG
Query on HG
Download SDF File 
Download CCD File 
C, D, E, F, G, I, J, N, O, P, R, S
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 192.994α = 90.00
b = 192.994β = 90.00
c = 493.202γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
XDSdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationCountryGrant Number
Slovenian Research AgencySloveniaP1-0391
BioStruct-XSloveniaFP7/2007-2013

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references