3ZXD | pdb_00003zxd

wild-type lysenin

PDB DOI: https://doi.org/10.2210/pdb3ZXD/pdb

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

Deposited: 2011-08-09 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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.236 (Depositor), 0.259 (DCC)
R-Value Work:
0.213 (Depositor), 0.236 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content

Total Structure Weight: 141.05 kDa
Atom Count: 9,376
Modeled Residue Count: 1,166
Deposited Residue Count: 1,236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSENIN	A, B, C, D	309	Eisenia fetida	Mutation(s): 0
UniProt
Find proteins for O18423 (Eisenia fetida) Explore O18423 Go to UniProtKB: O18423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O18423
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain N [auth A] SDF format, chain U [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B]	BA [auth D], N [auth A], U [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain N [auth A] Focus chain U [auth B] Interactions & Density Focus chain BA [auth D] Focus chain N [auth A] Focus chain U [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain S [auth B] mmCIF format, chain Y [auth D]	F [auth A] H [auth A] O [auth B] P [auth B] S [auth B] F [auth A], H [auth A], O [auth B], P [auth B], S [auth B], Y [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B] Focus chain Y [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain S [auth B] Focus chain Y [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain V [auth C] MOL2 format, chain E [auth A] MOL2 format, chain V [auth C] mmCIF format, chain E [auth A] mmCIF format, chain V [auth C]	E [auth A], V [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain V [auth C] Interactions & Density Focus chain E [auth A] Focus chain V [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain J [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D]	J [auth A] Q [auth B] R [auth B] W [auth C] X [auth C] J [auth A], Q [auth B], R [auth B], W [auth C], X [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain J [auth A] Focus chain Q [auth B] Focus chain R [auth B] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B]	AA [auth D] G [auth A] K [auth A] L [auth A] M [auth A] AA [auth D], G [auth A], K [auth A], L [auth A], M [auth A], T [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.236 (Depositor), 0.259 (DCC)
R-Value Work: 0.213 (Depositor), 0.236 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.91	α = 98.88
b = 85.56	β = 96.84
c = 108.81	γ = 90.04

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-09-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-19
Type: Initial release
Version 1.1: 2012-10-03
Changes: Database references
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description