3LEI

Lectin Domain of Lectinolysin complexed with Fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Structure of the lectin regulatory domain of the cholesterol-dependent cytolysin lectinolysin reveals the basis for its lewis antigen specificity.

Feil, S.C.Lawrence, S.Mulhern, T.D.Holien, J.K.Hotze, E.M.Farrand, S.Tweten, R.K.Parker, M.W.

(2012) Structure 20: 248-258

  • DOI: https://doi.org/10.1016/j.str.2011.11.017
  • Primary Citation of Related Structures:  
    3LE0, 3LEG, 3LEI, 3LEK

  • PubMed Abstract: 

    The cholesterol-dependent cytolysins (CDCs) punch holes in target cell membranes through a highly regulated process. Streptococcus mitis lectinolysin (LLY) exhibits another layer of regulation with a lectin domain that enhances the pore-forming activity of the toxin. We have determined the crystal structures of the lectin domain by itself and in complex with various glycans that reveal the molecular basis for the Lewis antigen specificity of LLY. A small-angle X-ray scattering study of intact LLY reveals the molecule is flat and elongated with the lectin domain oriented so that the Lewis antigen-binding site is exposed. We suggest that the lectin domain enhances the pore-forming activity of LLY by concentrating toxin molecules at fucose-rich sites on membranes, thus promoting the formation of prepore oligomers on the surface of susceptible cells.


  • Organizational Affiliation

    Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria 3065, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet aggregation factor Sm-hPAF153Streptococcus mitisMutation(s): 1 
Gene Names: samhpaf
UniProt
Find proteins for Q2PHL4 (Streptococcus mitis)
Explore Q2PHL4 
Go to UniProtKB:  Q2PHL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2PHL4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.01α = 90
b = 67.01β = 90
c = 97.8γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2010-12-29 
  • Deposition Author(s): Feil, S.C.

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-02-29
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2021-10-13
    Changes: Database references, Structure summary
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description