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Open data
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Basic information
Entry | Database: PDB / ID: 5i05 | ||||||||||||||||||||||||
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Title | Crystal structure of human BMP9 at 1.87 A resolution | ||||||||||||||||||||||||
![]() | Growth/differentiation factor 2 | ||||||||||||||||||||||||
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Function / homology | ![]() positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis ...positive regulation of epithelial cell differentiation / positive regulation of cartilage development / positive regulation of endothelial cell differentiation / positive regulation of bicellular tight junction assembly / Signaling by BMP / cellular response to BMP stimulus / activin receptor signaling pathway / positive regulation of BMP signaling pathway / cartilage development / blood vessel morphogenesis / negative regulation of endothelial cell migration / branching involved in blood vessel morphogenesis / negative regulation of DNA replication / positive regulation of Notch signaling pathway / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Saito, T. / Bokhove, M. / 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: ![]() Title: Crystal structure of BMP-9 and functional interactions with pro-region and receptors. Authors: Brown, M.A. / Zhao, Q. / Baker, K.A. / Naik, C. / Chen, C. / Pukac, L. / Singh, M. / Tsareva, T. / Parice, Y. / Mahoney, A. / Roschke, V. / Sanyal, I. / Choe, S. #2: ![]() Title: Structure of bone morphogenetic protein 9 procomplex. Authors: Mi, L.Z. / Brown, C.T. / Gao, Y. / Tian, Y. / Le, V.Q. / Walz, T. / Springer, T.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 | ![]() | 59.1 KB | Display | ![]() |
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PDB format | ![]() | 42.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5hzvC ![]() 5hzwC ![]() 5i04C ![]() 1kzkS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol![]() ![]() | ||||||||
Components on special symmetry positions |
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Components
#1: 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.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ![]() #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.77 % / Description: Rectangular Prism |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 1.0 M LiCl, 4% (v/v) PEG6000, 0.1 M NA-CITRATE / PH range: 3.0-4.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2014 |
Radiation | Monochromator: Si Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.87→41.36 Å / Num. obs: 15763 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.95 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.39 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1KZK Resolution: 1.87→41.36 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→41.36 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.6333 Å / Origin y: -10.984 Å / Origin z: -23.2336 Å
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Refinement TLS group | Selection details: chain A and (not resi 900:901) |