Macromolecule Content

Total Structure Weight: 76.27 kDa
Atom Count: 5210
Modelled Residue Count: 668
Deposited Residue Count: 692
Unique protein chains: 1

5I04

Crystal structure of the orphan region of human endoglin/CD105

PDB DOI: 10.2210/pdb5I04/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): Saito, T., Bokhove, M., de Sanctis, D., 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: 2.42 Å
R-Value Free: 0.263
R-Value Work: 0.220
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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

PubMed: 28564608 Search on PubMedSearch on PubMed Central
DOI: 10.1016/j.celrep.2017.05.011
Primary Citation of Related Structures:
5HZV, 5HZW, 5I04, 5I05

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.

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) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Endoglin	A	692	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 13 Gene Names: malE, b4034, JW3994, ENG, END
UniProt & NIH Common Fund Data Resources
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
PHAROS: P17813 GTEx: ENSG00000106991
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0AEX9P17813
Protein Feature View Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A	Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Ligand Interaction
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	D [auth A], E [auth A], F [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Ligand Interaction

Biologically Interesting Molecules (External Reference) 1 Unique

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

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 = 114.15	α = 90
b = 114.15	β = 90
c = 120.62	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Deposited Date: 2016-02-03
Released Date: 2017-06-07

Deposition Author(s):

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 (Full details and data files)

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