Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 68.66 kDa 
• Atom Count: 4626 
• Residue Count: 598 
• Unique protein chains: 1

5HZV

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

• DOI: 10.2210/pdb5HZV/pdb

• 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

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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 

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

• PubMed: 28564608 
• 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 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.

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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

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Organizational Affiliation: 

Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Huddinge 14183, Sweden. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Endoglin	A	626	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 13  Gene Names: malE, b4034, JW3994
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 GTEx  ENSG00000106991

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide /  Nutrient		--

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 = 125.16	α = 90
b = 125.16	β = 90
c = 88.54	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-02-03 
• Released Date: 2017-06-07 
Deposition Author(s): Bokhove, M., Saito, T., Jovine, L.

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Funding Organization	Location	Grant Number
Karolinska Institutet	Sweden	--
Center for Biosciences	Sweden	--
Swedish Research Council	Sweden	2012-5093
Gustafsson Foundation for Research in Natural Sciences and Medicine	Sweden	--
Sven and Ebba-Christina Hagberg foundation	Sweden	--
European Molecular Biology Organization		--
European Union		ERC 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