1XKU

Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the dimeric protein core of decorin, the archetypal small leucine-rich repeat proteoglycan

Scott, P.G.McEwan, P.A.Dodd, C.M.Bergmann, E.M.Bishop, P.N.Bella, J.

(2004) Proc Natl Acad Sci U S A 101: 15633-15638

  • DOI: 10.1073/pnas.0402976101
  • Primary Citation of Related Structures:  
    1XCD, 1XEC, 1XKU

  • PubMed Abstract: 
  • Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions ...

    Decorin is a ubiquitous extracellular matrix proteoglycan with a variety of important biological functions that are mediated by its interactions with extracellular matrix proteins, cytokines, and cell surface receptors. Decorin is the prototype of the family of small leucine-rich repeat proteoglycans and proteins (SLRPs), characterized by a protein core composed of leucine-rich repeats (LRRs), flanked by two cysteine-rich regions. We report here the crystal structure of the dimeric protein core of decorin, the best characterized member of the SLRP family. Each monomer adopts the curved solenoid fold characteristic of LRR domains, with a parallel beta-sheet on the inside interwoven with loops containing short segments of beta-strands, 3(10) helices, and polyproline II helices on the outside. Two main features are unique to this structure. First, decorin dimerizes through the concave surfaces of the LRR domains, which have been implicated previously in protein-ligand interactions. The amount of surface buried in this dimer rivals the buried surfaces of some of the highest-affinity macromolecular complexes reported to date. Second, the C-terminal region adopts an unusual capping motif that involves a laterally extended LRR and a disulfide bond. This motif seems to be unique to SLRPs and has not been observed in any other LRR protein structure to date. Possible implications of these features for decorin ligand binding and SLRP function are discussed.


    Related Citations: 
    • Light and X-ray scattering show decorin to be a dimer in solution
      Scott, P.G., Grossmann, J.G., Dodd, C.M., Sheehan, J.K., Bishop, P.N.
      (2003) J Biol Chem 278: 18353

    Organizational Affiliation

    Department of Biochemistry and Alberta Synchrotron Institute, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DecorinA330Bos taurusMutation(s): 0 
Gene Names: DCN
UniProt
Find proteins for P21793 (Bos taurus)
Explore P21793 
Go to UniProtKB:  P21793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.78α = 90
b = 124.145β = 90
c = 129.609γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary