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- PDB-2qjb: Crystal structure analysis of BMP-2 in complex with BMPR-IA varia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qjb | ||||||
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Title | Crystal structure analysis of BMP-2 in complex with BMPR-IA variant IA/IB | ||||||
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![]() | Cytokine/Receptor / ligand-receptor complex / Chondrogenesis / Cleavage on pair of basic residues / Cytokine / Developmental protein / Differentiation / Glycoprotein / Growth factor / Osteogenesis / ATP-binding / Disease mutation / Kinase / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphorylation / Serine/threonine-protein kinase / Transferase / Transmembrane / Cytokine-Receptor COMPLEX | ||||||
Function / homology | ![]() 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 / cardiac conduction system development / positive regulation of odontoblast differentiation / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kotzsch, A. / Mueller, T.D. | ||||||
![]() | ![]() Title: Structure analysis of bone morphogenetic protein-2 type I receptor complexes reveals a mechanism of receptor inactivation in juvenile polyposis syndrome. Authors: Kotzsch, A. / Nickel, J. / Seher, A. / Heinecke, K. / van Geersdaele, L. / Herrmann, T. / Sebald, W. / Mueller, T.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90 KB | Display | ![]() |
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PDB format | ![]() | 68.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.8 KB | Display | ![]() |
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Full document | ![]() | 474 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 23.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qj9C ![]() 2qjaC ![]() 1rewS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13126.128 Da / Num. of mol.: 2 / Fragment: mature part (residues 283-396) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 14770.498 Da / Num. of mol.: 2 / Fragment: extracellular domain (residues 24-152) Mutation: K88R,S90T,K92I,A93P,Q94H,L95Q,T98S,A74T,M78L,K79G,Y80L,D46E,G42H,A61T,I62M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 0.8M K Na phosphate, 25% ethylene glycol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 4, 2005 |
Radiation | Monochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→31.27 Å / Num. all: 21360 / Num. obs: 21360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.23 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.32 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.564 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1REW Resolution: 2.5→31.27 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.961 / SU ML: 0.152 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 81.516 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→31.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 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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