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Yorodumi- PDB-1rew: Structural refinement of the complex of bone morphogenetic protei... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rew | ||||||
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Title | Structural refinement of the complex of bone morphogenetic protein 2 and its type IA receptor | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR/SIGNALING PROTEIN / TGF-beta fold / BRIA-fold / 3-finger toxin fold / HORMONE-GROWTH FACTOR-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | Function and homology information neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / Mullerian duct regression / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development ...neural plate mediolateral regionalization / paraxial mesoderm structural organization / positive regulation of cardiac ventricle development / fibrous ring of heart morphogenesis / positive regulation of transforming growth factor beta2 production / Mullerian duct regression / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / heart formation / atrioventricular node cell development / negative regulation of aldosterone biosynthetic process / embryonic heart tube anterior/posterior pattern specification / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / mesendoderm development / negative regulation of steroid biosynthetic process / ameloblast differentiation / tricuspid valve morphogenesis / positive regulation of extracellular matrix constituent secretion / atrioventricular valve development / dorsal aorta morphogenesis / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / central nervous system neuron differentiation / corticotropin hormone secreting cell differentiation / cardiac right ventricle morphogenesis / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / pharyngeal arch artery morphogenesis / aortic valve development / telencephalon regionalization / positive regulation of odontogenesis / BMP binding / regulation of cardiac muscle cell proliferation / positive regulation of phosphatase activity / hindlimb morphogenesis / negative regulation of muscle cell differentiation / negative regulation of smooth muscle cell migration / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / lateral mesoderm development / regulation of lateral mesodermal cell fate specification / ventricular compact myocardium morphogenesis / pericardium development / pituitary gland development / lung vasculature development / mitral valve morphogenesis / BMP receptor complex / BMP receptor activity / dorsal/ventral axis specification / co-receptor binding / regulation of cellular senescence / neural crest cell development / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / transforming growth factor beta receptor activity, type I / ectoderm development / positive regulation of odontoblast differentiation / cardiac conduction system development / endocardial cushion formation / positive regulation of bone mineralization involved in bone maturation / phosphatase activator activity / Transcriptional regulation by RUNX2 / positive regulation of astrocyte differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / outflow tract septum morphogenesis / cardiac muscle tissue morphogenesis / ventricular trabecula myocardium morphogenesis / positive regulation of ossification / astrocyte differentiation / dorsal/ventral pattern formation / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / positive regulation of mesenchymal cell proliferation / endocardial cushion morphogenesis / embryonic digit morphogenesis / branching involved in ureteric bud morphogenesis / ventricular septum morphogenesis / negative regulation of fat cell differentiation / roof of mouth development / bone mineralization / outflow tract morphogenesis / positive regulation of osteoblast proliferation / SMAD binding / odontogenesis of dentin-containing tooth / somatic stem cell population maintenance Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.863 Å | ||||||
Authors | Keller, S. / Nickel, J. / Zhang, J.-L. / Sebald, W. / Mueller, T.D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Molecular recognition of BMP-2 and BMP receptor IA. Authors: Keller, S. / Nickel, J. / Zhang, J.L. / Sebald, W. / Mueller, T.D. #1: Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structure of the BMP-2-BRIA ectodomain complex Authors: Kirsch, T. / Sebald, W. / Dreyer, M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rew.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rew.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rew_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 1rew_full_validation.pdf.gz | 466.7 KB | Display | |
Data in XML | 1rew_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 1rew_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1rew ftp://data.pdbj.org/pub/pdb/validation_reports/re/1rew | HTTPS FTP |
-Related structure data
Related structure data | 1reuC 1es7S 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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Details | The assymmetric unit contains the biological active BMP-2 dimer and two BRIA monomers |
-Components
#1: Protein | Mass: 12923.854 Da / Num. of mol.: 2 / Fragment: mature part Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pN25c109 / Production host: Escherichia coli (E. coli) / References: UniProt: P12643 #2: Protein | Mass: 14674.451 Da / Num. of mol.: 2 / Fragment: extracellular domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32b / Production host: Escherichia coli (E. coli) / References: UniProt: P36894, EC: 2.7.1.37 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.88 Å3/Da / Density % sol: 68 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7 Details: sodium acetate, imidazole, glucose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 16, 2002 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→19.73 Å / Num. all: 54306 / Num. obs: 54306 / % possible obs: 96.8 % / Observed criterion σ(I): 1.2 / Redundancy: 4.6 % / Rsym value: 0.083 |
Reflection shell | Resolution: 1.86→1.91 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ES7 Resolution: 1.863→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.973 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.2 / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: REFMAC5
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.14 Å2
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Refine analyze | Luzzati coordinate error free: 0.109 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.863→19.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.863→1.911 Å / Total num. of bins used: 20
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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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