2D3R

Cratylia folibunda seed lectin at acidic pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structures of Cratylia floribunda seed lectin at acidic and basic pHs. Insights into the structural basis of the pH-dependent dimer-tetramer transition.

Del Sol, F.G.Cavada, B.S.Calvete, J.J.

(2007) J Struct Biol 158: 1-9

  • DOI: https://doi.org/10.1016/j.jsb.2006.08.014
  • Primary Citation of Related Structures:  
    2D3P, 2D3R

  • PubMed Abstract: 

    Structural determinants underlaying the pH-dependent dimer-tetramer transition of Diocleinae lectins were investigated from the structures of Cratylia floribunda seed lectin crystallized in conditions where it exist as a dimer (pH 4.6) or as a tetramer (pH 8.5). The acidic (aCFL) and the basic (bCFL) tetramers superimpose with overall r.m.s.d. of 0.53 A, though interdimer contacts are drastically reduced in aCFL, and the r.m.s.d. for the superposition of the 117-120 loops of aCFL vs. the bCFL tetramer is 1.29 A. Our data support the view that His51 plays a role in determining the conformation of the central cavity loops and that interdimer contacts involving ordered loop residues stabilize the canonical, pH-dependent tetramer. In the bCFL tetramer, hydrogen bonds between Asn118 and Thr120 of monomers A and D and residues Ser66, Ser108, Ser110, and Thr49 of the opposite monomer stabilize the canonical, pH-dependent tetrameric lectin structure. In CFL, Asn131 makes intradimer contacts with Asn122 and Ala123. In comparison, His131 in Dioclea grandiflora lectin establishes a network of interdimer interactions bridging the four central loops of the pH-independent tetramer. Our data provide new insights into the participation of specific amino acid residues in the mechanism of the quaternary association of Diocleinae lectins.


  • Organizational Affiliation

    Instituto de Biomedicina de Valencia, C.S.I.C., E-46010 Valencia, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin alpha chain
A, B, C, D
236Cratylia argenteaMutation(s): 0 
UniProt
Find proteins for P81517 (Cratylia argentea)
Explore P81517 
Go to UniProtKB:  P81517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81517
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.213α = 90
b = 125.44β = 90
c = 126.14γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations