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Yorodumi- PDB-5hzw: Crystal structure of the orphan region of human endoglin/CD105 in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hzw | ||||||||||||||||||||||||
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Title | Crystal structure of the orphan region of human endoglin/CD105 in complex with BMP9 | ||||||||||||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / ORPHAN DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR | ||||||||||||||||||||||||
Function / homology | Function and homology information 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 / negative regulation of nitric-oxide synthase activity / dorsal aorta morphogenesis / positive regulation of epithelial 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 / negative regulation of nitric-oxide synthase activity / dorsal aorta morphogenesis / positive regulation of epithelial cell differentiation / 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 / positive regulation of cartilage development / epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / transforming growth factor beta receptor activity / galactose binding / positive regulation of endothelial cell differentiation / positive regulation of systemic arterial blood pressure / regulation of transforming growth factor beta receptor signaling pathway / cardiac atrium morphogenesis / positive regulation of bicellular tight junction assembly / smooth muscle tissue development / type II transforming growth factor beta receptor binding / Signaling by BMP / activin binding / type I transforming growth factor beta receptor binding / cellular response to BMP stimulus / activin receptor signaling pathway / 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 / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / detection of maltose stimulus / maltose transport complex / negative regulation of DNA replication / positive regulation of Notch signaling pathway / heart looping / maltose binding / maltose transport / negative regulation of endothelial cell proliferation / maltodextrin transmembrane transport / positive regulation of SMAD protein signal transduction / carbohydrate transport / negative regulation of blood vessel endothelial cell migration / carbohydrate transmembrane transporter activity / positive regulation of collagen biosynthetic process / extracellular matrix disassembly / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / epithelial to mesenchymal transition / vasculogenesis / BMP signaling pathway / regulation of cell adhesion / coreceptor activity / positive regulation of endothelial cell proliferation / ATP-binding cassette (ABC) transporter complex / protein serine/threonine kinase activator activity / cell chemotaxis / ossification / negative regulation of angiogenesis / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / cytokine activity / cell motility / positive regulation of interleukin-8 production / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / wound healing / bone development / negative regulation of cell growth / osteoblast differentiation / cellular response to mechanical stimulus / positive regulation of angiogenesis / transmembrane signaling receptor activity / cell migration / regulation of cell population proliferation / outer membrane-bounded periplasmic space / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / periplasmic space / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / receptor complex / response to hypoxia / cell adhesion / response to xenobiotic stimulus / positive regulation of protein phosphorylation / external side of plasma membrane Similarity search - Function | ||||||||||||||||||||||||
Biological species | Escherichia coli K12 (bacteria) Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.451 Å | ||||||||||||||||||||||||
Authors | Bokhove, M. / Saito, T. / Jovine, L. | ||||||||||||||||||||||||
Funding support | Sweden, 7items
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Citation | Journal: Cell Rep / Year: 2017 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. Cell. Sci. / Year: 2007 Title: BMP-9 signals via ALK1 and inhibits bFGF-induced endothelial cell proliferation and VEGF-stimulated angiogenesis. Authors: Scharpfenecker, M. / van Dinther, M. / Liu, Z. / van Bezooijen, R.L. / Zhao, Q. / Pukac, L. / Lowik, C.W. / ten Dijke, P. #3: 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. #4: 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. #5: 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hzw.cif.gz | 438 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hzw.ent.gz | 364.8 KB | Display | PDB format |
PDBx/mmJSON format | 5hzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/5hzw ftp://data.pdbj.org/pub/pdb/validation_reports/hz/5hzw | HTTPS FTP |
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-Related structure data
Related structure data | 5hzvC 5i04SC 5i05SC 3sexS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 75141.164 Da / Num. of mol.: 1 Fragment: UNP Residues 27-393,UNP Residues 25-337,UNP Residues 27-393,UNP Residues 25-337 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 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.) Escherichia coli K12 (bacteria), (gene. exp.) Homo sapiens (human) Cell: Endothelial / Gene: malE, b4034, JW3994, ENG, END / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: P0AEX9, UniProt: P17813 |
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#2: Protein | Mass: 12102.971 Da / Num. of mol.: 1 / Fragment: UNP residues 320-429 Source method: isolated from a genetically manipulated source Details: Mature BMP9 / Source: (gene. exp.) Homo sapiens (human) / Gene: GDF2, BMP9 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9UK05 |
#3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#4: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.3 % / Description: Hexagonal Bipyramid |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.1 M AMMONIUM TARTRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97938 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014 |
Radiation | Monochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97938 Å / Relative weight: 1 |
Reflection | Resolution: 4.301→52.811 Å / Num. obs: 9558 / % possible obs: 100 % / Redundancy: 9.5 % / Biso Wilson estimate: 219 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.395 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 4.301→4.81 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 0.6 / CC1/2: 0.259 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3SEX, 5I04, 5I05 Resolution: 4.451→52.811 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.451→52.811 Å
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Refine LS restraints |
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LS refinement shell |
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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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