5Y03

Galectin-13/Placental Protein 13 variant R53H crystal structure

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 

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:  
    5XG7, 5XG8, 5Y03

  • 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 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 ...

    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. zhouyf383@nenu.edu.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Galactoside-binding soluble lectin 13 A142Homo sapiensMutation(s): 1 
Gene Names: LGALS13, PLAC8
Find proteins for Q9UHV8 (Homo sapiens)
Explore Q9UHV8 
Go to UniProtKB:  Q9UHV8
NIH Common Fund Data Resources
PHAROS:  Q9UHV8
GTEx:  ENSG00000105198
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.877α = 90
b = 92.314β = 90
c = 50.625γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2017-07-14 
  • Released Date: 2018-01-31 
    • Deposition Author(s): Wang, Y., Su, J.

Revision History  (Full details and data files)

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