3ZX7 | pdb_00003zx7

Complex of lysenin with phosphocholine

• PDB DOI: https://doi.org/10.2210/pdb3ZX7/pdb

• Classification: TOXIN
• Organism(s): Eisenia fetida
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-08-08 Released: 2012-09-19 
• Deposition Author(s): De Colibus, L., Sonnen, A.F.P., Morris, K.J., Siebert, C.A., Abrusci, P., Plitzko, J., Hodnik, V., Leippe, M., Volpi, E., Anderluh, G., Gilbert, R.J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 
  0.264 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structures of Lysenin Reveal a Shared Evolutionary Origin for Pore-Forming Proteins and its Mode of Sphingomyelin Recognition.

De Colibus, L., Sonnen, A.F.P., Morris, K.J., Siebert, C.A., Abrusci, P., Plitzko, J., Hodnik, V., Leippe, M., Volpi, E., Anderluh, G., Gilbert, R.J.C.

(2012) Structure 20: 1498

• PubMed: 22819216 
• DOI: https://doi.org/10.1016/j.str.2012.06.011
• Primary Citation Related Structures: 
  3ZX7, 3ZXD, 3ZXG


• PubMed Abstract: 
  

  Pore-forming proteins insert from solution into membranes to create lesions, undergoing a structural rearrangement often accompanied by oligomerization. Lysenin, a pore-forming toxin from the earthworm Eisenia fetida, specifically interacts with sphingomyelin (SM) and may confer innate immunity against parasites by attacking their membranes to form pores. SM has important roles in cell membranes and lysenin is a popular SM-labeling reagent. The structure of lysenin suggests common ancestry with other pore-forming proteins from a diverse set of eukaryotes and prokaryotes. The complex with SM shows the mode of its recognition by a protein in which both the phosphocholine headgroup and one acyl tail are specifically bound. Lipid interaction studies and assays using viable target cells confirm the functional reliance of lysenin on this form of SM recognition.

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Organizational Affiliation: 
• Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.41 kDa 
• Atom Count: 2,451 
• Modeled Residue Count: 296 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSENIN	A	309	Eisenia fetida	Mutation(s): 0
UniProt
Find proteins for O18423 (Eisenia fetida) Explore O18423  Go to UniProtKB:  O18423

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PC	G [auth A], K [auth A], L [auth A], M [auth A]	PHOSPHOCHOLINE C5 H15 N O4 P YHHSONZFOIEMCP-UHFFFAOYSA-O
PO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free:  0.264 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.11	α = 90
b = 98.11	β = 90
c = 184.17	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): De Colibus, L., Sonnen, A.F.P., Morris, K.J., Siebert, C.A., Abrusci, P., Plitzko, J., Hodnik, V., Leippe, M., Volpi, E., Anderluh, G., Gilbert, R.J.C.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2012-10-03
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary