9QVV | pdb_00009qvv

Crystal structure of the 4CHRD domain of human chordin, mutant designed to abolish binding to sulphated glycosaminoglycans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 
    0.279 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: in silico
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This is version 1.1 of the entry. See complete history

Literature

Structural and biophysical analysis of the four CHRD domains of human chordin reveals a novel binding site for glycosaminoglycans.

Snee, M.Birchenough, H.L.Becker, M.H.Popplewell, J.F.Ashe, H.L.Baldock, C.

(2026) J Biological Chem : 113248-113248

  • DOI: https://doi.org/10.1016/j.jbc.2026.113248
  • Primary Citation Related Structures: 
    9IGM, 9QVV, 9RD6

  • PubMed Abstract: 

    Chordin is a cysteine-rich protein which acts as a regulator of bone morphogenetic protein (BMP) signalling in the extracellular matrix. Acting in concert with twisted gastrulation (TWSG1), chordin works as an antagonist of BMP signalling by binding tightly to the growth factor and is a vital component of the network of interactions that establish developmental signalling gradients. Chordin is known to interact with BMP ligands via its four von-Willebrand factor type C domains, but the function of the large central four CHRD domains were previously unknown. Here we show that these domains interact strongly with sulphated glycosaminoglycans (GAGs) and provide evidence for the location of the binding site using X-ray crystallographic analysis combined with mutagenesis and biophysical techniques. Additionally, we report the first recombinant expression and purification of the complete functional chordin, TWSG1, BMP2, BMP7 complex which was used to demonstrate that the four CHRD domains are largely redundant with respect to the role of chordin as an inhibitor of BMP ligands. We therefore propose that the four CHRD domains of chordin have relevance in the diffusion and localisation of chordin-TWSG1-BMP complexes at the tissue and organismal level, mediated by their interaction with GAGs or proteoglycans.


  • Organizational Affiliation
    • Manchester Cell-Matrix Centre, Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.

Macromolecule Content 

  • Total Structure Weight: 54.83 kDa 
  • Atom Count: 3,628 
  • Modeled Residue Count: 478 
  • Deposited Residue Count: 503 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chordin503Homo sapiensMutation(s): 5 
Gene Names: CHRDUNQ217/PRO243
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2X0 (Homo sapiens)
Explore Q9H2X0 
Go to UniProtKB:  Q9H2X0
PHAROS:  Q9H2X0
GTEx:  ENSG00000090539 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2X0
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9H2X0-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH
GlyCosmos: G32152BH
GlyGen: G32152BH

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free:  0.279 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.142α = 90
b = 123.8β = 90
c = 123.787γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Database references