5U3E

Crystal Structure of Native Lectin from Canavalia bonariensis Seeds (CaBo) complexed with alpha-methyl-D-mannoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

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This is version 1.5 of the entry. See complete history


Literature

Canavalia bonariensis lectin: Molecular bases of glycoconjugates interaction and antiglioma potential.

Cavada, B.S.Silva, M.T.L.Osterne, V.J.S.Pinto-Junior, V.R.Nascimento, A.P.M.Wolin, I.A.V.Heinrich, I.A.Nobre, C.A.S.Moreira, C.G.Lossio, C.F.Rocha, C.R.C.Martins, J.L.Nascimento, K.S.Leal, R.B.

(2018) Int J Biol Macromol 106: 369-378

  • DOI: https://doi.org/10.1016/j.ijbiomac.2017.08.023
  • Primary Citation of Related Structures:  
    5U3E

  • PubMed Abstract: 

    CaBo is a mannose/glucose-specific lectin purified from seeds of Canavalia bonariensis. In the present work, we report the CaBo crystal structure determined to atomic resolution in the presence of X-man, a specific ligand. Similar to the structural characteristics of other legume lectins, CaBo presented the jellyroll motif, a metal binding site occupied by calcium and manganese ions close to the carbohydrate-recognition domain (CRD). In vitro test of CaBo cytotoxicity against glioma cells demonstrated its ability to decrease the cellular viability and migration by induction of autophagy and cell death. Molecular docking simulations corroborate previous data indicating that the lectin's biological activities occur mostly through interactions with glycoproteins since the lectin interacted favorably with several N-glycans, especially those of the high-mannose type. Together, these results suggest that CaBo interacts with glycosylated cell targets and elicits a remarkable antiglioma activity.


  • Organizational Affiliation

    Universidade Federal do Ceará, Fortaleza, Ceará, Brazil. Electronic address: bscavada@ufc.br.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Canavalia bonariensis seed lectin237Canavalia bonariensisMutation(s): 0 
UniProt
Find proteins for P58906 (Canavalia bonariensis)
Explore P58906 
Go to UniProtKB:  P58906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58906
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.169α = 90
b = 70.03β = 90
c = 111.649γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Data collection
  • Version 1.3: 2017-12-06
    Changes: Database references
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Refinement description, Structure summary