5I04

Crystal structure of the orphan region of human endoglin/CD105


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report



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:  
    5I05, 5I04, 5HZW, 5HZV

  • 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: 
    • Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells.
      Gougos, A., Letarte, M.
      (1990) J Biol Chem 265: 8361
    • Soluble endoglin specifically binds bone morphogenetic proteins 9 and 10 via its orphan domain, inhibits blood vessel formation, and suppresses tumor growth.
      Castonguay, R., Werner, E.D., Matthews, R.G., Presman, E., Mulivor, A.W., Solban, N., Sako, D., Pearsall, R.S., Underwood, K.W., Seehra, J., Kumar, R., Grinberg, A.V.
      (2011) J Biol Chem 286: 30034
    • Structural and functional insights into endoglin ligand recognition and binding.
      Alt, A., Miguel-Romero, L., Donderis, J., Aristorena, M., Blanco, F.J., Round, A., Rubio, V., Bernabeu, C., Marina, A.
      (2012) PLoS One 7: e29948
    • Endoglin requirement for BMP9 signaling in endothelial cells reveals new mechanism of action for selective anti-endoglin antibodies.
      Nolan-Stevaux, O., Zhong, W., Culp, S., Shaffer, K., Hoover, J., Wickramasinghe, D., Ruefli-Brasse, A.
      (2012) PLoS One 7: e50920

    Organizational Affiliation

    Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 14183, Sweden. Electronic address: luca.jovine@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,EndoglinA692Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 13 
Gene Names: malEb4034JW3994
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for P17813 (Homo sapiens)
Explore P17813 
Go to UniProtKB:  P17813
NIH Common Fund Data Resources
PHAROS  P17813
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PGE
Query on PGE

Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
Balpha-maltoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.15α = 90
b = 114.15β = 90
c = 120.62γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary