Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 166.09 kDa 
• Atom Count: 13127 
• Residue Count: 1443 
• Unique protein chains: 1

1HJX

Ligand-induced signalling and conformational change of the 39 kD glycoprotein from human articular chondrocytes

• DOI: 10.2210/pdb1HJX/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 2003-02-28 Released: 2003-03-11 
• Deposition Author(s): Houston, D.R., Recklies, A.D., Krupa, J.C., Van Aalten, D.M.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

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

• PubMed: 12775711 
• DOI: 10.1074/jbc.M303371200
• Primary Citation of Related Structures:  
  1HJX, 1HJW, 1HJV


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHITINASE-3 LIKE PROTEIN 1	A, B, C, D	362	Homo sapiens	Mutation(s): 1  Gene Names: CHI3L1
Find proteins for P36222 (Homo sapiens) Explore P36222  Go to UniProtKB:  P36222
NIH Common Fund Data Resources
PHAROS:  P36222 GTEx:  ENSG00000133048

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F, G, H	2		N-Glycosylation

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B, C, D	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.225 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.562	α = 90
b = 122.048	β = 90
c = 136.097	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
FFFEAR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-28 
• Released Date: 2003-03-11 
Deposition Author(s): Houston, D.R., Recklies, A.D., Krupa, J.C., Van Aalten, D.M.F.

Revision History 

• Version 1.0: 2003-03-11
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary