1G8W

IMPROVED STRUCTURE OF PHYTOHEMAGGLUTININ-L FROM THE KIDNEY BEAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.

Buts, L.Dao-Thi, M.H.Loris, R.Wyns, L.Etzler, M.Hamelryck, T.

(2001) J Mol Biol 309: 193-201

  • DOI: 10.1006/jmbi.2001.4639
  • Primary Citation of Related Structures:  
    1G7Y, 1G8W, 1G9F

  • PubMed Abstract: 
  • The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation, which becomes important when they interact with multivalent glycoconjugates, for instance those on cell surfaces ...

    The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation, which becomes important when they interact with multivalent glycoconjugates, for instance those on cell surfaces. Recently, it has become clear that certain lectins form weakly associated oligomers. This phenomenon may play a role in the regulation of receptor crosslinking and subsequent signal transduction. The crystal structure of DB58, a dimeric lectin from the legume Dolichos biflorus reveals a separate dimer of a previously unobserved type, in addition to a tetramer consisting of two such dimers. This tetramer resembles that formed by DBL, the seed lectin from the same plant. A single amino acid substitution in DB58 affects the conformation and flexibility of a loop in the canonical dimer interface. This disrupts the formation of a stable DBL-like tetramer in solution, but does not prohibit its formation in suitable conditions, which greatly increases the possibilities for the cross-linking of multivalent ligands. The non-canonical DB58 dimer has a buried symmetrical alpha helix, which can be present in the crystal in either of two antiparallel orientations. Two existing structures and datasets for lectins with similar quaternary structures were reconsidered. A central alpha helix could be observed in the soybean lectin, but not in the leucoagglutinating lectin from Phaseolus vulgaris. The relative position and orientation of the carbohydrate-binding sites in the DB58 dimer may affect its ability to crosslink mulitivalent ligands, compared to the other legume lectin dimers.


    Related Citations: 
    • The crystallographic structure of phytohemagglutinin-L
      Hamelryck, T.W., Dao-Thi, M., Poortmans, F., Chrispeels, M.J., Wyns, L., Loris, R.
      (1996) J Biol Chem 271: 20479
    • Crystallisation of glycosylated and non-glycosylated phytohemagglutinin-L
      Dao-Thi, M., Hamelryck, T.W., Poortmans, F., Voelker, T.A., Chrispeels, M.J., Wyns, L.
      (1996) Proteins 24: 134

    Organizational Affiliation

    ULTR-Ultrastructure Department, Vrije Universiteit Brussel, Sint-Genesius-Rode Belgium. lieven@ultr.vub.ac.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUCOAGGLUTINATING PHYTOHEMAGGLUTININA, B, C, D233Phaseolus vulgarisMutation(s): 0 
Gene Names: DLEC2
UniProt
Find proteins for P05087 (Phaseolus vulgaris)
Explore P05087 
Go to UniProtKB:  P05087
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.479α = 90
b = 121.278β = 93.18
c = 89.957γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MADNESSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-18
    Changes: Data collection
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary