5XG8

Galectin-13/Placental Protein 13 variant R53H crystal structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Galectin-13, a different prototype galectin, does not bind beta-galacto-sides and forms dimers via intermolecular disulfide bridges between Cys-136 and Cys-138

Su, J., Wang, Y., Si, Y., Gao, J., Song, C., Cui, L., Wu, R., Tai, G., Zhou, Y.

(2018) Sci Rep 8: 980-980

  • DOI: 10.1038/s41598-018-19465-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • During pregnancy, placental protein-13 (galectin-13) is highly expressed in the placenta and fetal tissue, and less so in maternal serum that is related to pre-eclampsia. To understand galectin-13 function at the molecular level, we solved its crysta ...

    During pregnancy, placental protein-13 (galectin-13) is highly expressed in the placenta and fetal tissue, and less so in maternal serum that is related to pre-eclampsia. To understand galectin-13 function at the molecular level, we solved its crystal structure and discovered that its dimer is stabilized by two disulfide bridges between Cys136 and Cys138 and six hydrogen bonds involving Val135, Val137, and Gln139. Native PAGE and gel filtration demonstrate that this is not a crystallization artifact because dimers also form in solution. Our biochemical studies indicate that galectin-13 ligand binding specificity is different from that of other galectins in that it does not bind β-galactosides. This is partly explained by the presence of Arg53 rather than His53 at the bottom of the carbohydrate binding site in a position that is crucial for interactions with β-galactosides. Mutating Arg53 to histidine does not re-establish normal β-galactoside binding, but rather traps cryoprotectant glycerol molecules within the ligand binding site in crystals of the R53H mutant. Moreover, unlike most other galectins, we also found that GFP-tagged galectin-13 is localized within the nucleus of HeLa and 293 T cells. Overall, galectin-13 appears to be a new type of prototype galectin with distinct properties.

    Organizational Affiliation: 

    Jilin Province Key Laboratory for Chemistry and Biology of Natural Drugs in Changbai Mountain, School of Life Sciences, Northeast Normal University, Changchun, 130024, PR China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galactoside-binding soluble lectin 13
A
138Homo sapiensMutation(s): 1 
Gene Names: LGALS13 (PLAC8)
Find proteins for Q9UHV8 (Homo sapiens)
Go to Gene View: LGALS13
Go to UniProtKB:  Q9UHV8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.171 
  • Space Group: C 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 58.037α = 90.00
b = 92.207β = 90.00
c = 50.703γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-04-12 
  • Released Date: 2018-01-31 
  • Deposition Author(s): Wang, Y., Su, J.Y.
Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31500637

Revision History 

  • Version 1.0: 2018-01-31
    Type: Initial release