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.




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