Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 39.64 kDa 
• Atom Count: 2996 
• Modelled Residue Count: 318 
• Deposited Residue Count: 356 
• Unique protein chains: 1

3WG3

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

• DOI: 10.2210/pdb3WG3/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Agrocybe cylindracea
• 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: 1.35 Å
• R-Value Free: 0.156 
• R-Value Work: 0.140 
• R-Value Observed: 0.141 

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: 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. 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactoside-binding lectin	A, B	178	Agrocybe cylindracea	Mutation(s): 0  EC: 3.1.21
UniProt
Find proteins for Q6WY08 (Agrocybe aegerita) Explore Q6WY08  Go to UniProtKB:  Q6WY08

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
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-glucopyranose	C, D	4		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900132	C, D	Blood group A H type 2 antigen, beta anomer	Oligosaccharide /  Antigen		--

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 = 102.921	α = 90
b = 102.921	β = 90
c = 74.694	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-25 
• 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, Structure summary
• Version 2.1: 2020-08-05
  Changes: Structure summary