3A0K

Crystal structure of an antiflamatory legume lectin from Cymbosema roseum seeds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.4 of the entry. See complete history


Literature

Structural basis for both pro- and anti-inflammatory response induced by mannose-specific legume lectin from Cymbosema roseum

Rocha, B.A.Delatorre, P.Oliveira, T.M.Benevides, R.G.Pires, A.F.Sousa, A.A.Souza, L.A.Ana Maria, S.A.Debray, H.de Azevedo, W.F.Sampaio, A.H.Cavada, B.S.

(2011) Biochimie 

  • DOI: https://doi.org/10.1016/j.biochi.2011.01.006
  • Primary Citation of Related Structures:  
    3A0K

  • PubMed Abstract: 

    Legume lectins, despite high sequence homology, express diverse biological activities that vary in potency and efficacy. In studies reported here, the mannose-specific lectin from Cymbosema roseum (CRLI), which binds N-glycoproteins, shows both pro-inflammatory effects when administered by local injection and anti-inflammatory effects when by systemic injection. Protein sequencing was obtained by Tandem Mass Spectrometry and the crystal structure was solved by X-ray crystallography using a Synchrotron radiation source. Molecular replacement and refinement were performed using CCP4 and the carbohydrate binding properties were described by affinity assays and computational docking. Biological assays were performed in order to evaluate the lectin edematogenic activity. The crystal structure of CRLI was established to a 1.8Å resolution in order to determine a structural basis for these differing activities. The structure of CRLI is closely homologous to those of other legume lectins at the monomer level and assembles into tetramers as do many of its homologues. The CRLI carbohydrate binding site was predicted by docking with a specific inhibitory trisaccharide. CRLI possesses a hydrophobic pocket for the binding of α-aminobutyric acid and that pocket is occupied in this structure as are the binding sites for calcium and manganese cations characteristic of legume lectins. CRLI route-dependent effects for acute inflammation are related to its carbohydrate binding domain (due to inhibition caused by the presence of α-methyl-mannoside), and are based on comparative analysis with ConA crystal structure. This may be due to carbohydrate binding site design, which differs at Tyr12 and Glu205 position.


  • Organizational Affiliation

    BioMol-Lab, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, P. O. Box 6043, 60.455-970 Fortaleza, Ceará, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cymbosema roseum mannose-specific lectinA,
B [auth C],
C [auth E],
D [auth G]
237Cymbosema roseumMutation(s): 0 
UniProt
Find proteins for D5MNX4 (Cymbosema roseum)
Explore D5MNX4 
Go to UniProtKB:  D5MNX4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5MNX4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ABA
Query on ABA

Download Ideal Coordinates CCD File 
K [auth E],
N [auth G]
ALPHA-AMINOBUTYRIC ACID
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth C],
I [auth E],
L [auth G]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
H [auth C],
J [auth E],
M [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.034α = 90
b = 103.074β = 90
c = 122.334γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-11
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection