4YCG

Pro-bone morphogenetic protein 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structure of bone morphogenetic protein 9 procomplex.

Mi, L.Z.Brown, C.T.Gao, Y.Tian, Y.Le, V.Q.Walz, T.Springer, T.A.

(2015) Proc.Natl.Acad.Sci.USA 112: 3710-3715

  • DOI: 10.1073/pnas.1501303112
  • Primary Citation of Related Structures:  
  • Also Cited By: 5I05

  • PubMed Abstract: 
  • Bone morphogenetic proteins (BMPs) belong to the TGF-β family, whose 33 members regulate multiple aspects of morphogenesis. TGF-β family members are secreted as procomplexes containing a small growth factor dimer associated with two larger prodomains ...

    Bone morphogenetic proteins (BMPs) belong to the TGF-β family, whose 33 members regulate multiple aspects of morphogenesis. TGF-β family members are secreted as procomplexes containing a small growth factor dimer associated with two larger prodomains. As isolated procomplexes, some members are latent, whereas most are active; what determines these differences is unknown. Here, studies on pro-BMP structures and binding to receptors lead to insights into mechanisms that regulate latency in the TGF-β family and into the functions of their highly divergent prodomains. The observed open-armed, nonlatent conformation of pro-BMP9 and pro-BMP7 contrasts with the cross-armed, latent conformation of pro-TGF-β1. Despite markedly different arm orientations in pro-BMP and pro-TGF-β, the arm domain of the prodomain can similarly associate with the growth factor, whereas prodomain elements N- and C-terminal to the arm associate differently with the growth factor and may compete with one another to regulate latency and stepwise displacement by type I and II receptors. Sequence conservation suggests that pro-BMP9 can adopt both cross-armed and open-armed conformations. We propose that interactors in the matrix stabilize a cross-armed pro-BMP conformation and regulate transition between cross-armed, latent and open-armed, nonlatent pro-BMP conformations.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA 02115.,Global BioTherapeutics Technologies, Pfizer Worldwide Research and Development, Cambridge, MA 02139; and.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115;,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115; Department of Molecular and Structural Biology, School of Life Sciences, Tianjin University, Tianjin 300072, China;,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115; Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, MA 02115; timothy.springer@childrens.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bone Morphogenetic Protein 9 Growth Factor Domain
A, B
296Mus musculusMutation(s): 0 
Gene Names: Gdf2 (Bmp9)
Find proteins for Q9WV56 (Mus musculus)
Go to UniProtKB:  Q9WV56
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Bone Morphogenetic Protein 9 Prodomain
C, D
110Homo sapiensMutation(s): 0 
Gene Names: GDF2 (BMP9)
Find proteins for Q9UK05 (Homo sapiens)
Go to Gene View: GDF2
Go to UniProtKB:  Q9UK05
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.780α = 90.00
b = 120.780β = 90.00
c = 220.620γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
RESOLVEphasing
SOLVEphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Type: Structure summary
  • Version 1.2: 2015-03-25
    Type: Database references
  • Version 1.3: 2015-04-01
    Type: Database references
  • Version 2.0: 2017-11-01
    Type: Atomic model, Author supporting evidence, Database references, Derived calculations, Source and taxonomy