Crystal Structure of Stabilin-1 Interacting Chitinase-Like Protein, SI-CLP

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.243 

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Structure of human stabilin-1 interacting chitinase-like protein (SI-CLP) reveals a saccharide-binding cleft with lower sugar-binding selectivity.

Meng, G.Zhao, Y.Bai, X.Liu, Y.Green, T.J.Luo, M.Zheng, X.

(2010) J Biol Chem 285: 39898-39904

  • DOI: https://doi.org/10.1074/jbc.M110.130781
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human secreted protein stabilin-1 interacting chitinase-like protein (SI-CLP) has been identified as a novel member of Glyco_18 domain-containing proteins that is involved in host defense and inflammatory reactions. Efficient secretion of SI-CLP is mediated by its interaction with the endocytic/sorting receptor stabilin-1. SI-CLP is expressed abundantly in macrophages and neutrophils and is up-regulated by Th2 cytokine IL-4 and glucocorticoid, which suggest that SI-CLP could be a marker for adverse effects of glucocorticoid therapy. To gain insight into the biological function of SI-CLP, we determined the crystal structure of SI-CLP at 2.7 Å resolution by x-ray crystallography and found that it featured a typical triose-phosphate isomerase barrel fold with a putative saccharide-binding cleft. Comparison with other chitinase-like proteins showed the cleft to be atypically wide and open. The saccharide-binding capacity of SI-CLP was investigated, and its ligand-binding specificity was found to relate to the length of the oligosaccharides, with preference for chitotetraose. Further investigations reveal that SI-CLP could bind LPS in vitro and neutralize its endotoxin effect on macrophages. Our results demonstrate the saccharide-binding property of SI-CLP by structure and in vitro biochemical analyses and suggest the possible roles of SI-CLP in pathogen sensing and endotoxin neutralization.

  • Organizational Affiliation

    National Laboratory of Protein Engineering and Plant Genetic Engineering, Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871, China

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chitinase domain-containing protein 1A [auth B],
B [auth A]
393Homo sapiensMutation(s): 0 
Gene Names: CHID1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BWS9 (Homo sapiens)
Explore Q9BWS9 
Go to UniProtKB:  Q9BWS9
GTEx:  ENSG00000177830 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BWS9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.243 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.11α = 90
b = 100.11β = 90
c = 249.97γ = 120
Software Package:
Software NamePurpose
SCALAdata processing
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations