3WOG

Crystal structure plant lectin in complex with ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Phytohemagglutinin from Phaseolus vulgaris (PHA-E) displays a novel glycan recognition mode using a common legume lectin fold

Nagae, M.Soga, K.Morita-Matsumoto, K.Hanashima, S.Ikeda, A.Yamamoto, K.Yamaguchi, Y.

(2014) Glycobiology 24: 368-378

  • DOI: https://doi.org/10.1093/glycob/cwu004
  • Primary Citation of Related Structures:  
    3WCR, 3WCS, 3WOG

  • PubMed Abstract: 

    Phytohemagglutinin from Phaseolus vulgaris (PHA-E), a legume lectin, has an unusual specificity toward biantennary galactosylated N-glycan with bisecting N-acetylglucosamine (GlcNAc). To investigate the interaction in detail, we have solved the crystal structures of PHA-E without ligand and in complex with biantennary N-glycan derivatives. PHA-E interacts with the trisaccharide unit (Galβ1-4GlcNAcβ1-2Man) in a manner completely different from that of mannose/glucose-specific legume lectins. The inner mannose residue binds to a novel site on the protein, and its rotation is opposite to that occurring in the monosaccharide-binding site of other lectins around the sugar O3 axis. Saturation-transfer difference NMR using biantennary di-galactosylated and bisected glycans reveals that PHA-E interacts with both antennas almost equally. The unique carbohydrate interaction explains the glycan-binding specificity and high affinity.


  • Organizational Affiliation

    Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN-Max Planck Joint Research Center, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Erythroagglutinin
A, B
254Phaseolus vulgarisMutation(s): 0 
UniProt
Find proteins for P05088 (Phaseolus vulgaris)
Explore P05088 
Go to UniProtKB:  P05088
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05088
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose
C, D
2N/A
Glycosylation Resources
GlyTouCan:  G85856KC
GlyCosmos:  G85856KC
GlyGen:  G85856KC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.78α = 90
b = 195.481β = 90
c = 97.829γ = 90
Software Package:
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-09
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary