+Open data
-Basic information
Entry | Database: PDB / ID: 5i05 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human BMP9 at 1.87 A resolution | ||||||||||||||||||||||||
Components | Growth/differentiation factor 2 | ||||||||||||||||||||||||
Keywords | SIGNALING PROTEIN / GROWTH DIFFERENTIATION FACTOR 2 / CELL PROLIFERATION SIGNAL / CYTOKINE / ANGIOGENESIS | ||||||||||||||||||||||||
Function / homology | Function and homology information 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 / negative regulation of endothelial cell migration / cartilage development ...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 / negative regulation of endothelial cell migration / cartilage development / blood vessel morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of endothelial cell proliferation / negative regulation of DNA replication / positive regulation of Notch signaling pathway / negative regulation of blood vessel endothelial cell migration / positive regulation of SMAD protein signal transduction / vasculogenesis / BMP signaling pathway / positive regulation of endothelial cell proliferation / protein serine/threonine kinase activator activity / ossification / negative regulation of angiogenesis / cytokine activity / positive regulation of interleukin-8 production / growth factor activity / negative regulation of cell growth / osteoblast differentiation / positive regulation of angiogenesis / angiogenesis / intracellular iron ion homeostasis / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||||||||||||||||||||
Authors | Saito, T. / Bokhove, M. / Jovine, L. | ||||||||||||||||||||||||
Funding support | Sweden, 7items
| ||||||||||||||||||||||||
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: 2005 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: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5i05.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5i05.ent.gz | 42.9 KB | Display | PDB format |
PDBx/mmJSON format | 5i05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/5i05 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/5i05 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5hzvC 5hzwC 5i04C 1kzkS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Symmetry | Point symmetry: (Schoenflies symbol: C2 (2 fold cyclic)) | ||||||||
Components on special symmetry positions |
|
-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.) Homo sapiens (human) / Cell: Endothelial / Gene: GDF2, BMP9 / Plasmid: pHLsec / Cell line (production host): HEK293S / Production host: Homo sapiens (human) / References: UniProt: Q9UK05 | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.81 Å3/Da / Density % sol: 67.77 % / Description: Rectangular Prism |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
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: 0.97949 Å / Relative weight: 1 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -10.6333 Å / Origin y: -10.984 Å / Origin z: -23.2336 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: chain A and (not resi 900:901) |