2D6O | pdb_00002d6o

Crystal structure of mouse galectin-9 N-terminal CRD in complex with N-acetyllactosamine dimer

• PDB DOI: https://doi.org/10.2210/pdb2D6O/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-14 Released: 2006-09-26 
• Deposition Author(s): Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Galectin-9 N-terminal Carbohydrate Recognition Domain from Mus musculus Reveals the Basic Mechanism of Carbohydrate Recognition

Nagae, M., Nishi, N., Murata, T., Usui, T., Nakamura, T., Wakatsuki, S., Kato, R.

(2006) J Biological Chem 281: 35884-35893

• PubMed: 16990264 
• DOI: https://doi.org/10.1074/jbc.M606648200
• Primary Citation Related Structures: 
  2D6K, 2D6L, 2D6M, 2D6N, 2D6O, 2D6P


• PubMed Abstract: 
  

  The galectins are a family of beta-galactoside-binding animal lectins with a conserved carbohydrate recognition domain (CRD). They have a high affinity for small beta-galactosides, but binding specificity for complex glycoconjugates varies considerably within the family. The ligand recognition is essential for their proper function, and the structures of several galectins have suggested their mechanism of carbohydrate binding. Galectin-9 has two tandem CRDs with a short linker, and we report the crystal structures of mouse galectin-9 N-terminal CRD (NCRD) in the absence and the presence of four ligand complexes. All structures form the same dimer, which is quite different from the canonical 2-fold symmetric dimer seen for galectin-1 and -2. The beta-galactoside recognition mechanism in the galectin-9 NCRD is highly conserved among other galectins. In the apo form structure, water molecules mimic the ligand hydrogen-bond network. The galectin-9 NCRD can bind both N-acetyllactosamine (Galbeta1-4GlcNAc) and T-antigen (Galbeta1-3GalNAc) with the proper location of Arg-64. Moreover, the structure of the N-acetyllactosamine dimer (Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc) complex shows a unique binding mode of galectin-9. Finally, surface plasmon resonance assay showed that the galectin-9 NCRD forms a homophilic dimer not only in the crystal but also in solution.

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Organizational Affiliation: 
• Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 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: 19.01 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 151 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
lectin, galactose binding, soluble 9	A [auth X]	159	Mus musculus	Mutation(s): 0
UniProt
Find proteins for O08573 (Mus musculus) Explore O08573  Go to UniProtKB:  O08573

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B [auth A]	4		N/A
Glycosylation Resources
GlyTouCan: G00058MO GlyCosmos: G00058MO GlyGen: G00058MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth X]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.212 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.796	α = 90
b = 94.422	β = 90
c = 56.544	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Nagae, M., Nishi, N., Nakamura, T., Murata, T., Wakatsuki, S., Kato, R.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-12-17
  Changes: Atomic model, Derived calculations
• Version 2.0: 2020-07-01
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 3.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 3.2: 2024-10-30
  Changes: Structure summary