Crystal structure of Bone Morphogenetic Protein-3 (BMP-3)

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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BMP-3 and BMP-6 Structures Illuminate the Nature of Binding Specificity with Receptors.

Allendorph, G.P.Isaacs, M.J.Kawakami, Y.Belmonte, J.C.Choe, S.

(2007) Biochemistry 46: 12238-12247

  • DOI: https://doi.org/10.1021/bi700907k
  • Primary Citation of Related Structures:  
    2QCQ, 2QCW

  • PubMed Abstract: 

    Bone morphogenetic proteins (BMPs) are extracellular messenger ligands involved in controlling a wide array of developmental and intercellular signaling processes. To initiate their specific intracellular signaling pathways, the ligands recognize and bind two structurally related serine/threonine kinase receptors, termed type I and type II, on the cell surface. Here, we present the crystal structures of BMP-3 and BMP-6, of which BMP-3 has remained poorly understood with respect to its receptor identity, affinity, and specificity. Using surface plasmon resonance (BIAcore) we show that BMP-3 binds Activin Receptor type II (ActRII) with Kd approximately 1.8 microM but ActRIIb with 30-fold higher affinity at Kd approximately 53 nM. This low affinity for ActRII may involve Ser-28 and Asp-33 of BMP-3, which are found only in BMP-3's type II receptor-binding interfaces. Point mutations of either residue to alanine results in up to 20-fold higher affinity to either receptor. We further demonstrate by Smad-based whole cell luciferase assays that the increased affinity of BMP-3S28A to ActRII enables the ligand's signaling ability to a level comparable to that of BMP-6. Focusing on BMP-3's preference for ActRIIb, we find that Lys-76 of ActRII and the structurally equivalent Glu-76 of ActRIIb are distinct between the two receptors. We demonstrate that ActRIIbE76K and ActRII bind BMP-3 with similar affinity, indicating BMP-3 receptor specificity is controlled by the interaction of Lys-30 of BMP-3 with Glu-76 of ActRIIb. These studies illustrate how a single amino acid can regulate the specificity of ligand-receptor binding and potentially alter biological signaling and function in vivo.

  • Organizational Affiliation

    Structural Biology Laboratory and Gene Expression Laboratory, Salk Institute for Biology Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bone morphogenetic protein 3
A, B
110Homo sapiensMutation(s): 0 
Gene Names: BMP3
UniProt & NIH Common Fund Data Resources
Find proteins for P12645 (Homo sapiens)
Explore P12645 
Go to UniProtKB:  P12645
PHAROS:  P12645
GTEx:  ENSG00000152785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12645
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.85α = 90
b = 96.85β = 90
c = 101.48γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description