2WQ4 | pdb_00002wq4

N-terminal domain of BC2L-C Lectin from Burkholderia cenocepacia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.166 (Depositor), 0.206 (DCC) 
  • R-Value Work: 
    0.131 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.133 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.5 of the entry. See complete history


Literature

A Tnf-Like Trimeric Lectin Domain from Burkholderia Cenocepacia with Specificity for Fucosylated Human Histo-Blood Group Antigens

Sulak, O.Cioci, G.Lahman, M.Delia, M.Varrot, A.Imberty, A.Wimmerova, M.

(2010) Structure 18: 59

  • DOI: https://doi.org/10.1016/j.str.2009.10.021
  • Primary Citation of Related Structures:  
    2WQ4

  • PubMed Abstract: 

    The opportunistic pathogen Burkholderia cenocepacia expresses several soluble lectins, among them BC2L-C. This lectin exhibits two domains: a C-terminal domain with high sequence similarity to the recently described calcium-dependent mannose-binding lectin BC2L-A, and an N-terminal domain of 156 amino acids without similarity to any known protein. The recombinant N-terminal BC2L-C domain is a new lectin with specificity for fucosylated human histo-blood group epitopes H-type 1, Lewis b, and Lewis Y, as determined by glycan array and isothermal titration calorimetry. Methylselenofucoside was used as ligand to solve the crystal structure of the N-terminal BC2L-C domain. Additional molecular modeling studies rationalized the preference for Lewis epitopes. The structure reveals a trimeric jellyroll arrangement with striking similarity to TNF-like proteins, and to BclA, the spore protein from Bacillus anthracis which may play an important role in bioadhesion of anthrax spores in human lungs.


  • Organizational Affiliation

    National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlárská 2, 611 37 Brno, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LECTIN
A, B, C
156Burkholderia cenocepacia J2315Mutation(s): 0 
UniProt
Find proteins for B4EH86 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610))
Explore B4EH86 
Go to UniProtKB:  B4EH86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB4EH86
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.166 (Depositor), 0.206 (DCC) 
  • R-Value Work:  0.131 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.133 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.1α = 90
b = 76.73β = 90
c = 103.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
HKL2Mapphasing
ARP/wARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SFUClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-12
    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: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Other, Refinement description, Structure summary
  • Version 1.5: 2024-10-16
    Changes: Data collection, Database references, Structure summary