5HZV

Crystal structure of the zona pellucida module of human endoglin/CD105

  • Classification: SIGNALING PROTEIN
  • Organism(s): Escherichia coli K-12, Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2016-02-03 Released: 2017-06-07 
  • Deposition Author(s): Bokhove, M., Saito, T., 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: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

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
    • A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
      Bork, P., Sander, C.
      (1992) FEBS Lett 300: 237
    • Zona pellucida domain proteins.
      Jovine, L., Darie, C.C., Litscher, E.S., Wassarman, P.M.
      (2005) Annu Rev Biochem 74: 83
    • Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
      Han, L., Monne, M., Okumura, H., Schwend, T., Cherry, A.L., Flot, D., Matsuda, T., Jovine, L.
      (2010) Cell 143: 404
    • A structured interdomain linker directs self-polymerization of human uromodulin.
      Bokhove, M., Nishimura, K., Brunati, M., Han, L., de Sanctis, D., Rampoldi, L., Jovine, L.
      (2016) Proc Natl Acad Sci U S A 113: 1552

    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,EndoglinA626Escherichia 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

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-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: 2.70 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.16α = 90
b = 125.16β = 90
c = 88.54γ = 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: 2017-08-23
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 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