Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C9  (3D View)
Global Stoichiometry: Homo 9-mer - A9 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C9  (3D View)
Global Stoichiometry: Homo 9-mer - A9 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 611.73 kDa 
• Atom Count: 41248 
• Modelled Residue Count: 5152 
• Deposited Residue Count: 5364 
• Unique protein chains: 1

5EC5

Crystal structure of lysenin pore

• PDB DOI: 10.2210/pdb5EC5/pdb

• Classification: TOXIN
• Organism(s): Eisenia fetida
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2015-10-20 Released: 2016-05-18 
• Deposition Author(s): Podobnik, M., Savory, P., Rojko, N., Kisovec, M., Bruce, M., Jayasinghe, L., Anderluh, G.
• Funding Organization(s): Slovenian Research Agency, BioStruct-X

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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 

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

• PubMed: 27176125 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysenin	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q [auth R], R [auth S]	298	Eisenia fetida	Mutation(s): 5  Membrane Entity: Yes
UniProt
Find proteins for O18423 (Eisenia fetida) Explore O18423  Go to UniProtKB:  O18423

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	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	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 = 192.994	α = 90
b = 192.994	β = 90
c = 493.202	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-10-20 
• Released Date: 2016-05-18 
Deposition Author(s): Podobnik, M., Savory, P., Rojko, N., Kisovec, M., Bruce, M., Jayasinghe, L., Anderluh, G.

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Funding Organization	Location	Grant Number
Slovenian Research Agency	Slovenia	P1-0391
BioStruct-X	Slovenia	FP7/2007-2013

Revision History  

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