3WG1

Crystal structure of Agrocybe cylindracea galectin with lactose

• PDB DOI: https://doi.org/10.2210/pdb3WG1/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Cyclocybe aegerita
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-25 Released: 2013-11-27 
• Deposition Author(s): Kuwabara, N., Hu, D., Tateno, H., Makio, H., Hirabayashi, J., Kato, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

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

• PubMed: 24036446 
• DOI: https://doi.org/10.1016/j.febslet.2013.08.046
• Primary Citation of Related Structures:  
  3WG1, 3WG2, 3WG3, 3WG4


• 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. We propose that the unique sequence provides these two distinct glycan-binding modes by an induced-fit mechanism.

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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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.69 kDa 
• Atom Count: 2,626 
• Modelled Residue Count: 320 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactoside-binding lectin	A, B	178	Cyclocybe aegerita	Mutation(s): 0
UniProt
Find proteins for Q6WY08 (Cyclocybe aegerita) Explore Q6WY08  Go to UniProtKB:  Q6WY08

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	C, D	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.368	α = 90
b = 125.368	β = 90
c = 56.589	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-27 
Deposition Author(s): Kuwabara, N., Hu, D., Tateno, H., Makio, H., Hirabayashi, J., Kato, R.

Revision History  

• 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, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary