4WVV

Chicken Galectin-8 N-terminal domain complexed with lactose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Combining Crystallography and Hydrogen-Deuterium Exchange to Study Galectin-Ligand Complexes.

Ruiz, F.M.Gilles, U.Lindner, I.Andre, S.Romero, A.Reusch, D.Gabius, H.J.

(2015) Chemistry 21: 13558-13568

  • DOI: https://doi.org/10.1002/chem.201501961
  • Primary Citation of Related Structures:  
    4WVV, 4WVW

  • PubMed Abstract: 

    The physiological significance arising from translating information stored in glycans into cellular effects explains the interest in structurally defining lectin-carbohydrate recognition. The relatively small set of adhesion/growth-regulatory galectins in chicken makes this system attractive to study the origins of specificity and divergence. Cell binding by using glycosylation mutants reveals binding of the N-terminal domain of chicken galectin-8 (CG-8N) to α-2,3-sialylated and galactose-terminated glycan chains. Cocrystals with lactose and its 3'-sialylated derivative disclose Arg58 as a key contact for the carboxylic acid and differences in loop lengths to the three homodimeric chicken galectins. Monitoring hydrogen-deuterium exchange by mass spectrometry revealed an effective reduction of deuteration after ligand binding within the contact area. In addition, evidence for changes in solvent accessibility of amide protons beyond this site was obtained. Their detection, which highlights the sensor capacity of this technique, encourages systematic studies on galectins and beyond.


  • Organizational Affiliation

    Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu, 9 28040 Madrid (Spain).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galectin145Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q1W2P6 (Gallus gallus)
Explore Q1W2P6 
Go to UniProtKB:  Q1W2P6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1W2P6
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan:  G88362QR
GlyCosmos:  G88362QR
GlyGen:  G88362QR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.459α = 90
b = 56.459β = 90
c = 201.239γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary