3WG3

Crystal structure of Agrocybe cylindracea galectin with blood type A antigen tetraose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Conformational change of a unique sequence in a fungal galectin from Agrocybe cylindracea controls glycan ligand-binding specificity.

Kuwabara, N.Hu, D.Tateno, H.Makyio, H.Hirabayashi, J.Kato, R.

(2013) FEBS Lett 587: 3620-3625

  • DOI: 10.1016/j.febslet.2013.08.046
  • Primary Citation of Related Structures:  
    3WG3, 3WG4, 3WG1, 3WG2

  • PubMed Abstract: 
  • A fungal galectin from Agrocybe cylindracea (ACG) exhibits broad binding specificity for β-galactose-containing glycans. We determined the crystal structures of wild-type ACG and the N46A mutant, with and without glycan ligands. From these structures and a saccharide-binding analysis of the N46A mutant, we revealed that a conformational change of a unique insertion sequence containing Asn46 provides two binding modes for ACG, and thereby confers broad binding specificity ...

    A fungal galectin from Agrocybe cylindracea (ACG) exhibits broad binding specificity for β-galactose-containing glycans. We determined the crystal structures of wild-type ACG and the N46A mutant, with and without glycan ligands. From these structures and a saccharide-binding analysis of the N46A mutant, we revealed that a conformational change of a unique insertion sequence containing Asn46 provides two binding modes for ACG, and thereby confers broad binding specificity. We propose that the unique sequence provides these two distinct glycan-binding modes by an induced-fit mechanism.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galactoside-binding lectinA, B178Agrocybe cylindraceaMutation(s): 0 
EC: 3.1.21
UniProt
Find proteins for Q6WY08 (Agrocybe aegerita)
Explore Q6WY08 
Go to UniProtKB:  Q6WY08
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D4 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
F [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900132
Query on PRD_900132
C, DBlood group A H type 2 antigen, beta anomerOligosaccharide /  Antigen

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.156 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.141 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.921α = 90
b = 102.921β = 90
c = 74.694γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-27
    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: 2020-08-05
    Changes: Structure summary