Crystal structure analysis of Bone Morphogenetic Protein-6 (BMP-6)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 

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Type I receptor binding of bone morphogenetic protein 6 is dependent on N-glycosylation of the ligand.

Saremba, S.Nickel, J.Seher, A.Kotzsch, A.Sebald, W.Mueller, T.D.

(2007) FEBS J 275: 172-183

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.06187.x
  • Primary Citation of Related Structures:  
    2R52, 2R53

  • PubMed Abstract: 

    Bone morphogenetic proteins (BMPs), together with transforming growth factor (TGF)-beta and activins/inhibins, constitute the TGF-beta superfamily of ligands. This superfamily is formed by more than 30 structurally related secreted proteins. The crystal structure of human BMP-6 was determined to a resolution of 2.1 A; the overall structure is similar to that of other TGF-beta superfamily ligands, e.g. BMP-7. The asymmetric unit contains the full dimeric BMP-6, indicating possible asymmetry between the two monomeric subunits. Indeed, the conformation of several loops differs between both monomers. In particular, the prehelix loop, which plays a crucial role in the type I receptor interactions of BMP-2, adopts two rather different conformations in BMP-6, indicating possible dynamic flexibility of the prehelix loop in its unbound conformation. Flexibility of this loop segment has been discussed as an important feature required for promiscuous binding of different type I receptors to BMPs. Further studies investigating the interaction of BMP-6 with different ectodomains of type I receptors revealed that N-glycosylation at Asn73 of BMP-6 in the wrist epitope is crucial for recognition by the activin receptor type I. In the absence of the carbohydrate moiety, activin receptor type I-mediated signaling of BMP-6 is totally diminished. Thus, flexibility within the binding epitope of BMP-6 and an unusual recognition motif, i.e. an N-glycosylation motif, possibly play an important role in type I receptor specificity of BMP-6.

  • Organizational Affiliation

    Lehrstuhl für Physiologische Chemie II, Biozentrum der Universität Würzburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bone morphogenetic protein 6
A, B
143Homo sapiensMutation(s): 0 
Gene Names: BMP6VGR
UniProt & NIH Common Fund Data Resources
Find proteins for P22004 (Homo sapiens)
Explore P22004 
Go to UniProtKB:  P22004
PHAROS:  P22004
GTEx:  ENSG00000153162 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22004
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.240 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.655α = 90
b = 97.655β = 90
c = 85.048γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description