5LFN image
Entry Detail
PDB ID:
5LFN
Keywords:
Title:
Crystal structure of human chondroadherin
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2016-07-03
Release Date:
2016-12-28
Method Details:
Experimental Method:
Resolution:
2.10 Å
R-Value Free:
0.26
R-Value Work:
0.24
R-Value Observed:
0.24
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Chondroadherin
Chain IDs:A, B, C, D
Chain Length:337
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Crystal structure of human chondroadherin: solving a difficult molecular-replacement problem using de novo models.
Acta Crystallogr D Struct Biol 73 53 63 (2017)
PMID: 28045385 DOI: 10.1107/S205979831601980X

Abstact

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.

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