Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 168.59 kDa 
• Atom Count: 12269 
• Residue Count: 1448 
• Unique protein chains: 1

1NWT

Crystal structure of human cartilage gp39 (HC-gp39) in complex with chitopentaose

• DOI: 10.2210/pdb1NWT/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2003-02-06 Released: 2003-08-26 
• Deposition Author(s): Fusetti, F., Pijning, T., Kalk, K.H., Bos, E., Dijkstra, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Crystal structure and carbohydrate-binding properties of the human cartilage glycoprotein-39

Fusetti, F., Pijning, T., Kalk, K.H., Bos, E., Dijkstra, B.W.

(2003) J Biol Chem 278: 37753-37760

• PubMed: 12851408 
• DOI: 10.1074/jbc.M303137200
• Primary Citation of Related Structures:  
  1NWU, 1NWT, 1NWS, 1NWR


• PubMed Abstract: 
  

The human cartilage glycoprotein-39 (HCgp-39 or YKL40) is expressed by synovial cells and macrophages during inflammation. Its precise physiological role is unknown. However, it has been proposed that HCgp-39 acts as an autoantigen in rheumatoid arthritis, and high expression levels have been associated with cancer development. HCgp-39 shares high sequence homology with family 18 chitinases, and although it binds to chitin it lacks enzymatic activity. The crystal structure of HCgp-39 shows that the protein displays a (beta/alpha)8-barrel fold with an insertion of an alpha + beta domain. A 43-A long carbohydrate-binding cleft is present at the C-terminal side of the beta-strands in the (beta/alpha)8 barrel. Binding of chitin fragments of different lengths identified nine sugar-binding subsites in the groove. Protein-carbohydrate interactions are mainly mediated by stacking of side chains of aromatic amino acid residues. Surprisingly, the specificity of chitin binding to HCgp-39 depends on the length of the oligosaccharide. Although chitin disaccharides tend to occupy the distal subsites, longer chains bind preferably to the central subsites in the groove. Despite the absence of enzymatic activity, long chitin fragments are distorted upon binding, with the GlcNAc at subsite -1 in a boat conformation, similar to what has been observed in chitinases. The presence of chitin in the human body has never been documented so far. However, the binding features observed in the complex structures suggest that either chitin or a closely related oligosaccharide could act as the physiological ligand for HCgp-39.

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Organizational Affiliation: 

Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands.

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): 0  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, G, I, K	2		N-Glycosylation

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, J, L	6		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-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-alpha-D-glucopyranose	H	5		N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.253 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.32	α = 90
b = 128.32	β = 90
c = 108.58	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-06 
• Released Date: 2003-08-26 
Deposition Author(s): Fusetti, F., Pijning, T., Kalk, K.H., Bos, E., Dijkstra, B.W.

Revision History 

• Version 1.0: 2003-08-26
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2018-04-04
  Changes: Advisory, Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary