1W3G | pdb_00001w3g

Hemolytic lectin from the mushroom Laetiporus sulphureus complexed with two N-acetyllactosamine molecules.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 
    0.280 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.1 of the entry. See complete history

Literature

Structural Analysis of the Laetiporus Sulphureus Hemolytic Pore-Forming Lectin in Complex with Sugars

Mancheno, J.M.Tateno, H.Goldstein, I.J.Martinez-Ripoll, M.Hermoso, J.A.

(2005) J Biological Chem 280: 17251

  • DOI: https://doi.org/10.1074/jbc.M413933200
  • Primary Citation Related Structures: 
    1W3A, 1W3F, 1W3G

  • PubMed Abstract: 

    LSL is a lectin produced by the parasitic mushroom Laetiporus sulphureus, which exhibits hemolytic and hemagglutinating activities. Here, we report the crystal structure of LSL refined to 2.6-A resolution determined by the single isomorphous replacement method with the anomalous scatter (SIRAS) signal of a platinum derivative. The structure reveals that LSL is hexameric, which was also shown by analytical ultracentrifugation. The monomeric protein (35 kDa) consists of two distinct modules: an N-terminal lectin module and a pore-forming module. The lectin module has a beta-trefoil scaffold that bears structural similarities to those present in toxins known to interact with galactose-related carbohydrates such as the hemagglutinin component (HA1) of the progenitor toxin from Clostridium botulinum, abrin, and ricin. On the other hand, the C-terminal pore-forming module (composed of domains 2 and 3) exhibits three-dimensional structural resemblances with domains 3 and 4 of the beta-pore-forming toxin aerolysin from the Gram-negative bacterium Aeromonas hydrophila, and domains 2 and 3 from the epsilon-toxin from Clostridium perfringens. This finding reveals the existence of common structural elements within the aerolysin-like family of toxins that could be directly involved in membrane-pore formation. The crystal structures of the complexes of LSL with lactose and N-acetyllactosamine reveal two dissacharide-binding sites per subunit and permits the identification of critical residues involved in sugar binding.


  • Organizational Affiliation
    • Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Rocasolano, CSIC, Serrano, 119, 28006 Madrid, Spain. xjosemi@iqfr.csic.es

Macromolecule Content 

  • Total Structure Weight: 36.26 kDa 
  • Atom Count: 2,667 
  • Modeled Residue Count: 313 
  • Deposited Residue Count: 315 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HEMOLYTIC LECTIN FROM LAETIPORUS SULPHUREUS315Laetiporus sulphureusMutation(s): 0 
UniProt
Find proteins for Q7Z8V1 (Laetiporus sulphureus)
Explore Q7Z8V1 
Go to UniProtKB:  Q7Z8V1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z8V1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
B, C
2N/A
Glycosylation Resources
GlyTouCan: G79333MY
GlyCosmos: G79333MY
GlyGen: G79333MY

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free:  0.280 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.72α = 90
b = 101.72β = 90
c = 192.91γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary