7AG0

Complex between the bone morphogenetic protein 2 and its antagonist Noggin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of the interaction between human cytokine BMP-2 and the antagonist Noggin reveals molecular details of cell chondrogenesis inhibition.

Robert, C.Kerff, F.Bouillenne, F.Gavage, M.Vandevenne, M.Filee, P.Matagne, A.

(2023) J Biol Chem 299: 102892-102892

  • DOI: https://doi.org/10.1016/j.jbc.2023.102892
  • Primary Citation of Related Structures:  
    7AG0

  • PubMed Abstract: 

    Bone morphogenetic proteins (BMPs) are secreted cytokines belonging to the transforming growth factor-β superfamily. New therapeutic approaches based on BMP activity, particularly for cartilage and bone repair, have sparked considerable interest; however, a lack of understanding of their interaction pathways and the side effects associated with their use as biopharmaceuticals have dampened initial enthusiasm. Here, we used BMP-2 as a model system to gain further insight into both the relationship between structure and function in BMPs and the principles that govern affinity for their cognate antagonist Noggin. We produced BMP-2 and Noggin as inclusion bodies in Escherichia coli and developed simple and efficient protocols for preparing pure and homogeneous (in terms of size distribution) solutions of the native dimeric forms of the two proteins. The identity and integrity of the proteins were confirmed using mass spectrometry. Additionally, several in vitro cell-based assays, including enzymatic measurements, RT-qPCR, and matrix staining, demonstrated their biological activity during cell chondrogenic and hypertrophic differentiation. Furthermore, we characterized the simple 1:1 noncovalent interaction between the two ligands (K D ca. 0.4 nM) using bio-layer interferometry and solved the crystal structure of the complex using X-ray diffraction methods. We identified the residues and binding forces involved in the interaction between the two proteins. Finally, results obtained with the BMP-2 N102D mutant suggest that Noggin is remarkably flexible and able to accommodate major structural changes at the BMP-2 level. Altogether, our findings provide insights into BMP-2 activity and reveal the molecular details of its interaction with Noggin.


  • Organizational Affiliation

    Laboratory of Enzymology and Protein Folding, University of Liège, Liège, Belgium; Centre for Protein Engineering, InBioS Research Unit, University of Liège, Liège, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Noggin206Homo sapiensMutation(s): 0 
Gene Names: NOG
UniProt & NIH Common Fund Data Resources
Find proteins for Q13253 (Homo sapiens)
Explore Q13253 
Go to UniProtKB:  Q13253
PHAROS:  Q13253
GTEx:  ENSG00000183691 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13253
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bone morphogenetic protein 2114Homo sapiensMutation(s): 0 
Gene Names: BMP2BMP2A
UniProt & NIH Common Fund Data Resources
Find proteins for P12643 (Homo sapiens)
Explore P12643 
Go to UniProtKB:  P12643
PHAROS:  P12643
GTEx:  ENSG00000125845 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12643
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.31α = 90
b = 103.31β = 90
c = 170.13γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Walloon RegionBelgium#16100518 AUTOBMP-2

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-13
    Type: Initial release
  • Version 1.1: 2023-04-26
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description