5LFN

Crystal structure of human chondroadherin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem using de novo models.

Ramisch, S.Pramhed, A.Tillgren, V.Aspberg, A.Logan, D.T.

(2017) Acta Crystallogr D Struct Biol 73: 53-63

  • DOI: 10.1107/S205979831601980X

  • PubMed Abstract: 
  • Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen a ...

    Chondroadherin (CHAD) is a cartilage matrix protein that mediates the adhesion of isolated chondrocytes. Its protein core is composed of 11 leucine-rich repeats (LRR) flanked by cysteine-rich domains. CHAD makes important interactions with collagen as well as with cell-surface heparin sulfate proteoglycans and α2β1 integrins. The integrin-binding site is located in a region of hitherto unknown structure at the C-terminal end of CHAD. Peptides based on the C-terminal human CHAD (hCHAD) sequence have shown therapeutic potential for treating osteoporosis. This article describes a still-unconventional structure solution by phasing with de novo models, the first of a β-rich protein. Structure determination of hCHAD using traditional, though nonsystematic, molecular replacement was unsuccessful in the hands of the authors, possibly owing to a combination of low sequence identity to other LRR proteins, four copies in the asymmetric unit and weak translational pseudosymmetry. However, it was possible to solve the structure by generating a large number of de novo models for the central LRR domain using Rosetta and multiple parallel molecular-replacement attempts using AMPLE. The hCHAD structure reveals an ordered C-terminal domain belonging to the LRRCT fold, with the integrin-binding motif (WLEAK) being part of a regular α-helix, and suggests ways in which experimental therapeutic peptides can be improved. The crystal structure itself and docking simulations further support that hCHAD dimers form in a similar manner to other matrix LRR proteins.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray diffraction analysis of human chondroadherin.
      Pramhed, A.,Addis, L.,Tillgren, V.,Wenglen, C.,Heinegard, D.,Logan, D.T.
      (2008) Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64: 516


    Organizational Affiliation

    Department of Biochemistry and Structural Biology, Lund University, Box 124, SE-221 00 Lund, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chondroadherin
A, B, C, D
337Homo sapiensMutation(s): 0 
Gene Names: CHAD (SLRR4A)
Find proteins for O15335 (Homo sapiens)
Go to Gene View: CHAD
Go to UniProtKB:  O15335
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.245 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.480α = 90.00
b = 111.590β = 92.22
c = 128.680γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
AMPLEphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-01-25
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Data collection