3QDY

Structure of the hexagonal form of the Boletus edulis lectin in complex with T-antigen disaccharide and N,N-diacetyl chitobiose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a lectin with antitumoral properties in king bolete (Boletus edulis) mushrooms.

Bovi, M.Carrizo, M.E.Capaldi, S.Perduca, M.Chiarelli, L.R.Galliano, M.Monaco, H.L.

(2011) Glycobiology 21: 1000-1009

  • DOI: 10.1093/glycob/cwr012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A novel lectin has been isolated from the fruiting bodies of the common edible mushroom Boletus edulis (king bolete, penny bun, porcino or cep) by affinity chromatography on a chitin column. We propose for the lectin the name BEL (B. edulis lectin). ...

    A novel lectin has been isolated from the fruiting bodies of the common edible mushroom Boletus edulis (king bolete, penny bun, porcino or cep) by affinity chromatography on a chitin column. We propose for the lectin the name BEL (B. edulis lectin). BEL inhibits selectively the proliferation of several malignant cell lines and binds the neoplastic cell-specific T-antigen disaccharide, Galβ1-3GalNAc. The lectin was structurally characterized: the molecule is a homotetramer and the 142-amino acid sequence of the chains was determined. The protein belongs to the saline-soluble family of mushroom fruiting body-specific lectins. BEL was also crystallized and its three-dimensional structure was determined by X-ray diffraction to 1.15 Å resolution. The structure is similar to that of Agaricus bisporus lectin. Using the appropriate co-crystals, the interactions of BEL with specific mono- and disaccharides were also studied by X-ray diffraction. The six structures of carbohydrate complexes reported here provide details of the interactions of the ligands with the lectin and shed light on the selectivity of the two distinct binding sites present in each protomer.


    Organizational Affiliation

    Biocrystallography Laboratory, Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie 15, 37134 Verona, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BOLETUS EDULIS LECTIN
A, B
143Boletus edulisMutation(s): 0 
Find proteins for F2Z266 (Boletus edulis)
Go to UniProtKB:  F2Z266
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
A2G
Query on A2G

Download SDF File 
Download CCD File 
A, B
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
 Ligand Interaction
CBS
Query on CBS

Download SDF File 
Download CCD File 
A, B
DI(N-ACETYL-D-GLUCOSAMINE)
C16 H28 N2 O11
CDOJPCSDOXYJJF-KSKNGZLJSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.192 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 124.045α = 90.00
b = 124.045β = 90.00
c = 104.473γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
ADSCdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-11-02
    Type: Database references