5I05

Crystal structure of human BMP9 at 1.87 A resolution

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens

  • Deposited: 2016-02-03 Released: 2017-06-07 
  • Deposition Author(s): Saito, T., Bokhove, M., Jovine, L.
  • Funding Organization(s): Karolinska Institutet; Center for Biosciences; Swedish Research Council; Gustafsson Foundation for Research in Natural Sciences and Medicine; Sven and Ebba-Christina Hagberg foundation; European Molecular Biology Organization; European Union 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1.

Saito, T.Bokhove, M.Croci, R.Zamora-Caballero, S.Han, L.Letarte, M.de Sanctis, D.Jovine, L.

(2017) Cell Rep 19: 1917-1928

  • DOI: 10.1016/j.celrep.2017.05.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endoglin (ENG)/CD105 is an essential endothelial cell co-receptor of the transforming growth factor β (TGF-β) superfamily, mutated in hereditary hemorrhagic telangiectasia type 1 (HHT1) and involved in tumor angiogenesis and preeclampsia. Here, we pr ...

    Endoglin (ENG)/CD105 is an essential endothelial cell co-receptor of the transforming growth factor β (TGF-β) superfamily, mutated in hereditary hemorrhagic telangiectasia type 1 (HHT1) and involved in tumor angiogenesis and preeclampsia. Here, we present crystal structures of the ectodomain of human ENG and its complex with the ligand bone morphogenetic protein 9 (BMP9). BMP9 interacts with a hydrophobic surface of the N-terminal orphan domain of ENG, which adopts a new duplicated fold generated by circular permutation. The interface involves residues mutated in HHT1 and overlaps with the epitope of tumor-suppressing anti-ENG monoclonal TRC105. The structure of the C-terminal zona pellucida module suggests how two copies of ENG embrace homodimeric BMP9, whose binding is compatible with ligand recognition by type I but not type II receptors. These findings shed light on the molecular basis of the BMP signaling cascade, with implications for future therapeutic interventions in this fundamental pathway.


    Related Citations: 
    • 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
    • Crystal structure of BMP-9 and functional interactions with pro-region and receptors.
      Brown, M.A.,Zhao, Q.,Baker, K.A.,Naik, C.,Chen, C.,Pukac, L.,Singh, M.,Tsareva, T.,Parice, Y.,Mahoney, A.,Roschke, V.,Sanyal, I.,Choe, S.
      (2005) J. Biol. Chem. 280: 25111


    Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 14183, Sweden.,Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 14183, Sweden. Electronic address: luca.jovine@ki.se.,ESRF-The European Synchrotron, Grenoble 38000, France.,Molecular Medicine, Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, University of Toronto, Toronto, ON M5G 0A4, Canada; Department of Immunology, University of Toronto, Toronto, ON M5G 0A4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Growth/differentiation factor 2
A
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.213 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.060α = 90.00
b = 71.060β = 90.00
c = 145.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Karolinska InstitutetSweden--
Center for BiosciencesSweden--
Swedish Research CouncilSweden2012-5093
Gustafsson Foundation for Research in Natural Sciences and MedicineSweden--
Sven and Ebba-Christina Hagberg foundationSweden--
European Molecular Biology Organization--
European UnionERC 260759

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence