5MX1 | pdb_00005mx1

Crystal structure of human chondroadherin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 
    0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5MX1

This is version 1.3 of the entry. See complete history

Literature

Structural and functional analysis of two small leucine-rich repeat proteoglycans, fibromodulin and chondroadherin.

Paracuellos, P.Kalamajski, S.Bonna, A.Bihan, D.Farndale, R.W.Hohenester, E.

(2017) Matrix Biol 63: 106-116

  • DOI: https://doi.org/10.1016/j.matbio.2017.02.002
  • Primary Citation Related Structures: 
    5MX0, 5MX1

  • PubMed Abstract: 

    The small leucine-rich proteoglycans (SLRPs) are important regulators of extracellular matrix assembly and cell signalling. We have determined crystal structures at ~2.2Å resolution of human fibromodulin and chondroadherin, two collagen-binding SLRPs. Their overall fold is similar to that of the prototypical SLRP, decorin, but unlike decorin neither fibromodulin nor chondroadherin forms a stable dimer. A previously identified binding site for integrin α2β1 maps to an α-helix in the C-terminal cap region of chondroadherin. Interrogation of the Collagen Toolkits revealed a unique binding site for chondroadherin in collagen II, and no binding to collagen III. A triple-helical peptide containing the sequence GAOGPSGFQGLOGPOGPO (O is hydroxyproline) forms a stable complex with chondroadherin in solution. In fibrillar collagen I and II, this sequence is aligned with the collagen cross-linking site KGHR, suggesting a role for chondroadherin in cross-linking.


  • Organizational Affiliation
    • Department of Life Sciences, Imperial College London, London, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 77.92 kDa 
  • Atom Count: 5,640 
  • Modeled Residue Count: 654 
  • Deposited Residue Count: 684 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chondroadherin
A, B
342Homo sapiensMutation(s): 0 
Gene Names: CHADSLRR4A
UniProt & NIH Common Fund Data Resources
Find proteins for O15335 (Homo sapiens)
Explore O15335 
Go to UniProtKB:  O15335
PHAROS:  O15335
GTEx:  ENSG00000136457 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15335
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.194 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.45α = 90
b = 60.7β = 100.6
c = 57.66γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101748/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary