1M4U

Crystal structure of Bone Morphogenetic Protein-7 (BMP-7) in complex with the secreted antagonist Noggin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report



Literature

Structural Basis of BMP Signalling Inhibition by the Cystine Knot Protein Noggin

Groppe, J.Greenwald, J.Wiater, E.Rodriguez-Leon, J.Economides, A.N.Kwiatkowski, W.Affolter, M.Vale, W.W.Izpisua-Belmonte, J.C.Choe, S.

(2002) Nature 420: 636-642

  • DOI: 10.1038/nature01245
  • Primary Citation of Related Structures:  
    1M4U

  • PubMed Abstract: 
  • The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as diverse as establishment of the embryonic dorsal-ventral axis, induction of neural tissue, formation of joints in the skele ...

    The interplay between bone morphogenetic proteins (BMPs) and their antagonists governs developmental and cellular processes as diverse as establishment of the embryonic dorsal-ventral axis, induction of neural tissue, formation of joints in the skeletal system and neurogenesis in the adult brain. So far, the three-dimensional structures of BMP antagonists and the structural basis for inactivation have remained unknown. Here we report the crystal structure of the antagonist Noggin bound to BMP-7, which shows that Noggin inhibits BMP signalling by blocking the molecular interfaces of the binding epitopes for both type I and type II receptors. The BMP-7-binding affinity of site-specific variants of Noggin is correlated with alterations in bone formation and apoptosis in chick limb development, showing that Noggin functions by sequestering its ligand in an inactive complex. The scaffold of Noggin contains a cystine (the oxidized form of cysteine) knot topology similar to that of BMPs; thus, ligand and antagonist seem to have evolved from a common ancestral gene.


    Related Citations: 
    • Three-dimensional structure of recombinant human osteogenic protein 1: Structural paradigm for the transforming growth factor beta superfamily
      Griffith, D.L., Keck, P.C., Sampath, T.K., Rueger, D.C., Carlson, W.D.
      (1996) Proc Natl Acad Sci U S A 93: 878

    Organizational Affiliation

    Structural Biology, Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NogginA206Homo sapiensMutation(s): 0 
Gene Names: NOG
Find proteins for Q13253 (Homo sapiens)
Explore Q13253 
Go to UniProtKB:  Q13253
NIH Common Fund Data Resources
PHAROS  Q13253
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bone Morphogenetic Protein-7L139Homo sapiensMutation(s): 0 
Gene Names: BMP7OP1
Find proteins for P18075 (Homo sapiens)
Explore P18075 
Go to UniProtKB:  P18075
NIH Common Fund Data Resources
PHAROS  P18075
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.834α = 90
b = 99.834β = 90
c = 150.327γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
REFMACrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary