1HJV

Crystal structure of hcgp-39 in complex with chitin tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 2.2 of the entry. See complete history


Literature

Structure and Ligand-Induced Conformational Change of the 39-kDa Glycoprotein from Human Articular Chondrocytes.

Houston, D.R.Recklies, A.D.Krupa, J.C.Van Aalten, D.M.F.

(2003) J Biol Chem 278: 30206

  • DOI: https://doi.org/10.1074/jbc.M303371200
  • Primary Citation of Related Structures:  
    1HJV, 1HJW, 1HJX

  • PubMed Abstract: 

    The 39-kDa human cartilage glycoprotein (HCGP39), a member of a novel family of chitinase-like lectins (Chilectins), is overexpressed in articular chondrocytes and certain cancers. Proposed functions of this protein include a role in connective tissue remodeling and defense against pathogens. Similar to other Chi-lectins, HCGP39 promotes the growth of connective tissue cells. The ability of HCGP39 to activate cytoplasmic signaling pathways suggests the presence of a ligand for this protein at the cell surface. There is currently no information regarding the identity of any physiological or pathological ligands of the Chi-lectins or the nature of the protein-ligand interaction. Here, we show that HCGP39 is able to bind chitooligosaccharides with micromolar affinity. Crystal structures of the native protein and a complex with GlcNAc8 show that the ligand is bound in identical fashion to family 18 chitinases. However, unlike the chitinases, binding of the oligosaccharide ligand to HCGP39 induces a large conformational change. Thus, HCGP39 could be a lectin that binds chitin-like oligosaccharide ligands and possibly plays a role in innate responses to chitinous pathogens, such as fungi and nematodes.


  • Organizational Affiliation

    Division of Biological Chemistry & Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CHITINASE-3 LIKE PROTEIN 1
A, B, C, D
362Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P36222 (Homo sapiens)
Explore P36222 
Go to UniProtKB:  P36222
PHAROS:  P36222
GTEx:  ENSG00000133048 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36222
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P36222-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, G, I, K
3N/A
Glycosylation Resources
GlyTouCan:  G47362BJ
GlyCosmos:  G47362BJ
GlyGen:  G47362BJ
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, H, J, L
4N/A
Glycosylation Resources
GlyTouCan:  G01361SX
GlyCosmos:  G01361SX
GlyGen:  G01361SX
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
M [auth A],
Q [auth B],
U [auth C],
Y [auth D]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
N [auth A]
O [auth A]
P [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.253 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.645α = 90
b = 123.321β = 90
c = 135.486γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2012-08-22
    Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary