5EC5

Crystal structure of lysenin pore


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 

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: https://doi.org/10.1038/ncomms11598
  • Primary Citation of Related Structures:  
    5EC5

  • 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 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

    Oxford Nanopore Technologies Ltd., Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford Science Park, Oxford OX4 4GA, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysenin298Eisenia fetidaMutation(s): 5 
Membrane Entity: Yes 
UniProt
Find proteins for O18423 (Eisenia fetida)
Explore O18423 
Go to UniProtKB:  O18423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO18423
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO

Download Ideal Coordinates CCD File 
AA [auth E]
AB [auth S]
DA [auth F]
EA [auth G]
GA [auth H]
AA [auth E],
AB [auth S],
DA [auth F],
EA [auth G],
GA [auth H],
HA [auth H],
JA [auth I],
MA [auth K],
NA [auth K],
OA [auth L],
PA [auth L],
QA [auth M],
RA [auth M],
S [auth A],
T [auth A],
U [auth B],
UA [auth O],
V [auth B],
W [auth C],
XA [auth P],
Y [auth D],
YA [auth R]
MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
HG
Query on HG

Download Ideal Coordinates CCD File 
BA [auth E]
BB [auth S]
CA [auth F]
FA [auth G]
IA [auth I]
BA [auth E],
BB [auth S],
CA [auth F],
FA [auth G],
IA [auth I],
KA [auth J],
LA [auth J],
SA [auth N],
TA [auth N],
VA [auth O],
WA [auth P],
X [auth C],
Z [auth D],
ZA [auth R]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.217 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.994α = 90
b = 192.994β = 90
c = 493.202γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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