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Open data
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Basic information
Entry | Database: PDB / ID: 5i04 | ||||||||||||||||||||||||
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Title | Crystal structure of the orphan region of human endoglin/CD105 | ||||||||||||||||||||||||
![]() | Maltose-binding periplasmic protein,Endoglin | ||||||||||||||||||||||||
![]() | SIGNALING PROTEIN / ORPHAN DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR | ||||||||||||||||||||||||
Function / homology | ![]() extracellular matrix constituent secretion / atrial cardiac muscle tissue morphogenesis / detection of hypoxia / atrioventricular canal morphogenesis / vascular associated smooth muscle cell development / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / negative regulation of nitric-oxide synthase activity / positive regulation of vascular associated smooth muscle cell differentiation ...extracellular matrix constituent secretion / atrial cardiac muscle tissue morphogenesis / detection of hypoxia / atrioventricular canal morphogenesis / vascular associated smooth muscle cell development / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / negative regulation of nitric-oxide synthase activity / positive regulation of vascular associated smooth muscle cell differentiation / cell migration involved in endocardial cushion formation / central nervous system vasculogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / transforming growth factor beta receptor activity / galactose binding / regulation of transforming growth factor beta receptor signaling pathway / cardiac atrium morphogenesis / positive regulation of systemic arterial blood pressure / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / type I transforming growth factor beta receptor binding / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / regulation of phosphorylation / positive regulation of BMP signaling pathway / glycosaminoglycan binding / transforming growth factor beta binding / signaling receptor activator activity / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / detection of maltose stimulus / maltose transport complex / heart looping / negative regulation of endothelial cell proliferation / carbohydrate transport / positive regulation of SMAD protein signal transduction / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / positive regulation of collagen biosynthetic process / extracellular matrix disassembly / epithelial to mesenchymal transition / vasculogenesis / regulation of cell adhesion / BMP signaling pathway / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / cell chemotaxis / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / bone development / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / cell migration / regulation of cell population proliferation / outer membrane-bounded periplasmic space / periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / nuclear body / cell adhesion / response to hypoxia / response to xenobiotic stimulus / positive regulation of protein phosphorylation / external side of plasma membrane / negative regulation of gene expression / focal adhesion / DNA damage response / positive regulation of gene expression / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Saito, T. / Bokhove, M. / de Sanctis, D. / Jovine, L. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1. Authors: Saito, T. / Bokhove, M. / Croci, R. / Zamora-Caballero, S. / Han, L. / Letarte, M. / de Sanctis, D. / Jovine, L. #1: Journal: J. Biol. Chem. / Year: 1990 Title: Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells. Authors: Gougos, A. / Letarte, M. #2: Journal: J. Biol. Chem. / Year: 2011 Title: Soluble endoglin specifically binds bone morphogenetic proteins 9 and 10 via its orphan domain, inhibits blood vessel formation, and suppresses tumor growth. Authors: 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. #3: Journal: PLoS ONE / Year: 2012 Title: Structural and functional insights into endoglin ligand recognition and binding. Authors: Alt, A. / Miguel-Romero, L. / Donderis, J. / Aristorena, M. / Blanco, F.J. / Round, A. / Rubio, V. / Bernabeu, C. / Marina, A. #4: Journal: PLoS ONE / Year: 2012 Title: Endoglin requirement for BMP9 signaling in endothelial cells reveals new mechanism of action for selective anti-endoglin antibodies. Authors: Nolan-Stevaux, O. / Zhong, W. / Culp, S. / Shaffer, K. / Hoover, J. / Wickramasinghe, D. / Ruefli-Brasse, A. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 275.4 KB | Display | ![]() |
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PDB format | ![]() | 221.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 848 KB | Display | ![]() |
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Full document | ![]() | 851.5 KB | Display | |
Data in XML | ![]() | 24.2 KB | Display | |
Data in CIF | ![]() | 32.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hzvC ![]() 5hzwC ![]() 5i05C ![]() 3setS ![]() 3sexS ![]() 4wrnS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 75254.336 Da / Num. of mol.: 1 Mutation: I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, ...Mutation: I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N,I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A, R422N Source method: isolated from a genetically manipulated source Details: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, ...Details: THIS PROTEIN IS A CHIMERA. RESIDUES 56-422 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I57T, D137A, K138A, E227A, N228A, A270H, K274H, K294A, A367V, I372V, E414A, E417A, D418A AND R422N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 426-737 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 26-337 OF SWISS-PROT DATABASE ENTRY P17813. SUBTRACTING 400 FROM THE PDB ENTRY RESIDUE NUMBERING RESULTS IN THE NUMBERING ACCORDING TO UNIPROT ENTRY P17813. Source: (gene. exp.) ![]() ![]() ![]() Cell: Endothelial / Gene: malE, b4034, JW3994, ENG, END / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: ![]() | ||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose | ||
#3: Sugar | ChemComp-NAG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 57.8 % / Description: Droplet |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 1000, 0.1 M TRIS-HCL / PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2014 |
Radiation | Monochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.42→45.74 Å / Num. obs: 33737 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 70.03 Å2 / Rsym value: 0.046 / Net I/σ(I): 11.76 |
Reflection shell | Resolution: 2.42→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.811 / Mean I/σ(I) obs: 1.25 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SEX, 3SET, 4WRN Resolution: 2.42→45.737 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 35.15
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.42→45.737 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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