3I8T

N-terminal CRD1 domain of mouse Galectin-4 in complex with lactose

• PDB DOI: https://doi.org/10.2210/pdb3I8T/pdb

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


• Deposited: 2009-07-10 Released: 2011-02-23 
• Deposition Author(s): Brynda, J., Krejcirikova, V., Rezacova, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Structure of the mouse galectin-4 N-terminal carbohydrate-recognition domain reveals the mechanism of oligosaccharide recognition

Krejcirikova, V., Pachl, P., Fabry, M., Maly, P., Rezacova, P., Brynda, J.

(2011) Acta Crystallogr D Biol Crystallogr 67: 204-211

• PubMed: 21358051 
• DOI: https://doi.org/10.1107/S0907444911004082
• Primary Citation of Related Structures:  
  3I8T


• PubMed Abstract: 
  

  Galectin-4, a member of the tandem-repeat subfamily of galectins, participates in cell-membrane interactions and plays an important role in cell adhesion and modulation of immunity and malignity. The oligosaccharide specificity of the mouse galectin-4 carbohydrate-recognition domains (CRDs) has been reported previously. In this work, the structure and binding properties of the N-terminal domain CRD1 were further investigated and the crystal structure of CRD1 in complex with lactose was determined at 2.1 Å resolution. The lactose-binding affinity was characterized by fluorescence measurements and two lactose-binding sites were identified: a high-affinity site with a K(d) value in the micromolar range (K(d1) = 600 ± 70 µM) and a low-affinity site with K(d2) = 28 ± 10 mM.

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Organizational Affiliation: 

Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, vvi, Prague, Czech Republic.

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 19.44 kDa 
• Atom Count: 1,302 
• Modelled Residue Count: 140 
• Deposited Residue Count: 164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galectin-4	A	164	Mus musculus	Mutation(s): 0  Gene Names: gal-4, Lgals4
UniProt
Find proteins for Q8K419 (Mus musculus) Explore Q8K419  Go to UniProtKB:  Q8K419

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G88362QR GlyCosmos:  G88362QR GlyGen:  G88362QR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900008	B	alpha-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.224 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.841	α = 90
b = 90.841	β = 90
c = 57.104	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Brynda, J., Krejcirikova, V., Rezacova, P.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-30
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary