4YCG

Pro-bone morphogenetic protein 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

wwPDB Validation 3D Report Full Report



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 U S A 112: 3710-3715

  • DOI: 10.1073/pnas.1501303112
  • Primary Citation of Related Structures:  
    4YCG, 4YCI

  • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bone Morphogenetic Protein 9 Growth Factor DomainAB296Mus musculusMutation(s): 0 
Gene Names: Gdf2Bmp9
Find proteins for Q9WV56 (Mus musculus)
Explore Q9WV56 
Go to UniProtKB:  Q9WV56
NIH Common Fund Data Resources
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bone Morphogenetic Protein 9 ProdomainCD110Homo sapiensMutation(s): 0 
Gene Names: GDF2BMP9
Find proteins for Q9UK05 (Homo sapiens)
Explore Q9UK05 
Go to UniProtKB:  Q9UK05
NIH Common Fund Data Resources
PHAROS  Q9UK05
Protein Feature View
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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
E, F
2 N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.78α = 90
b = 120.78β = 90
c = 220.62γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Structure summary
  • Version 1.2: 2015-03-25
    Changes: Database references
  • Version 1.3: 2015-04-01
    Changes: Database references
  • Version 2.0: 2017-11-01
    Changes: Atomic model, Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary