3NBD

Clitocybe nebularis ricin B-like lectin (CNL) in complex with lactose, crystallized at pH 7.1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Bivalent carbohydrate binding is required for biological activity of Clitocybe nebularis lectin (CNL), the N,N'-diacetyllactosediamine (GalNAc beta 1-4GlcNAc, LacdiNAc)-specific lectin from basidiomycete C. nebularis

Pohleven, J.Renko, M.Magister, S.Smith, D.F.Kunzler, M.Strukelj, B.Turk, D.Kos, J.Sabotic, J.

(2012) J.Biol.Chem. 287: 10602-10612

  • DOI: 10.1074/jbc.M111.317263
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lectins are carbohydrate-binding proteins that exert their biological activity by binding to specific cell glycoreceptors. We have expressed CNL, a ricin B-like lectin from the basidiomycete Clitocybe nebularis in Escherichia coli. The recombinant le ...

    Lectins are carbohydrate-binding proteins that exert their biological activity by binding to specific cell glycoreceptors. We have expressed CNL, a ricin B-like lectin from the basidiomycete Clitocybe nebularis in Escherichia coli. The recombinant lectin, rCNL, agglutinates human blood group A erythrocytes and is specific for the unique glycan N,N'-diacetyllactosediamine (GalNAcβ1-4GlcNAc, LacdiNAc) as demonstrated by glycan microarray analysis. We here describe the crystal structures of rCNL in complex with lactose and LacdiNAc, defining its interactions with the sugars. CNL is a homodimeric lectin, each of whose monomers consist of a single ricin B lectin domain with its β-trefoil fold and one carbohydrate-binding site. To study the mode of CNL action, a nonsugar-binding mutant and nondimerizing monovalent CNL mutants that retain carbohydrate-binding activity were prepared. rCNL and the mutants were examined for their biological activities against Jurkat human leukemic T cells and the hypersensitive nematode Caenorhabditis elegans mutant strain pmk-1. rCNL was toxic against both, although the mutants were inactive. Thus, the bivalent carbohydrate-binding property of homodimeric CNL is essential for its activity, providing one of the rare pieces of evidence that certain activities of lectins are associated with their multivalency.


    Organizational Affiliation

    Department of Biotechnology, JoŽef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia. jure.pohleven@ijs.si




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ricin B-like lectin
A, B
148Clitocybe nebularisMutation(s): 0 
Find proteins for B2ZRS9 (Clitocybe nebularis)
Go to UniProtKB:  B2ZRS9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
LBT
Query on LBT

Download SDF File 
Download CCD File 
A, B
ALPHA-LACTOSE
C12 H22 O11
GUBGYTABKSRVRQ-XLOQQCSPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.119α = 90.00
b = 85.080β = 90.00
c = 97.629γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
AMoREphasing
REFMACrefinement
MAR345dtbdata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2012-03-07
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Advisory, Refinement description