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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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

  • 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.USA 93: 878

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bone Morphogenetic Protein-7
L
139Homo sapiensMutation(s): 0 
Gene Names: BMP7 (OP1)
Find proteins for P18075 (Homo sapiens)
Go to Gene View: BMP7
Go to UniProtKB:  P18075
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Noggin
A
206Homo sapiensMutation(s): 0 
Gene Names: NOG
Find proteins for Q13253 (Homo sapiens)
Go to Gene View: NOG
Go to UniProtKB:  Q13253
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.241 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 99.834α = 90.00
b = 99.834β = 90.00
c = 150.327γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CCP4data scaling
MLPHAREphasing
REFMACrefinement
HKL-2000data collection
TRUNCATEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-18
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance