+Open data
-Basic information
Entry | Database: PDB / ID: 3bmp | |||||||||
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Title | HUMAN BONE MORPHOGENETIC PROTEIN-2 (BMP-2) | |||||||||
Components | PROTEIN (BONE MORPHOGENETIC PROTEIN 2 (BMP-2)) | |||||||||
Keywords | CYTOKINE / BONE MORPHOGENETIC PROTEIN / CYSTIN-KNOT / TGFB-FAMILY | |||||||||
Function / homology | Function and homology information cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / embryonic heart tube anterior/posterior pattern specification / negative regulation of steroid biosynthetic process ...cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly development / negative regulation of aldosterone biosynthetic process / atrioventricular canal morphogenesis / negative regulation of cortisol biosynthetic process / mesenchymal cell proliferation involved in ureteric bud development / embryonic heart tube anterior/posterior pattern specification / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / negative regulation of cardiac muscle cell differentiation / regulation of odontogenesis of dentin-containing tooth / endodermal-mesodermal cell signaling / corticotropin hormone secreting cell differentiation / negative regulation of insulin-like growth factor receptor signaling pathway / thyroid-stimulating hormone-secreting cell differentiation / mesenchyme development / aortic valve development / telencephalon regionalization / positive regulation of odontogenesis / positive regulation of phosphatase activity / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / pericardium development / lung vasculature development / BMP receptor complex / co-receptor binding / telencephalon development / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / BMP receptor binding / 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 / Signaling by BMP / cellular response to BMP stimulus / cardiac muscle cell differentiation / cardiac muscle tissue morphogenesis / astrocyte differentiation / positive regulation of ossification / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / positive regulation of p38MAPK cascade / endocardial cushion morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of fat cell differentiation / bone mineralization / positive regulation of osteoblast proliferation / odontogenesis of dentin-containing tooth / positive regulation of SMAD protein signal transduction / inner ear development / cellular response to organic cyclic compound / negative regulation of cell cycle / positive regulation of Wnt signaling pathway / epithelial to mesenchymal transition / positive regulation of fat cell differentiation / cell fate commitment / chondrocyte differentiation / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of bone mineralization / positive regulation of epithelial to mesenchymal transition / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / animal organ morphogenesis / negative regulation of smooth muscle cell proliferation / response to bacterium / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / protein destabilization / bone development / negative regulation of canonical Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / positive regulation of miRNA transcription / osteoblast differentiation / Regulation of RUNX2 expression and activity / positive regulation of protein binding / cell-cell signaling / heart development / in utero embryonic development / transcription by RNA polymerase II / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / positive regulation of apoptotic process Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Scheufler, C. / Sebald, W. / Huelsmeyer, M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of human bone morphogenetic protein-2 at 2.7 A resolution. Authors: Scheufler, C. / Sebald, W. / Hulsmeyer, M. #1: Journal: Eur.J.Biochem. / Year: 1996 Title: Human Bone Morphogenetic Protein 2 Contains a Heparin-Binding Site which Modifies its Biological Activity Authors: Ruppert, R. / Hoffmann, E. / Sebald, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bmp.cif.gz | 35.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bmp.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 3bmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/3bmp ftp://data.pdbj.org/pub/pdb/validation_reports/bm/3bmp | HTTPS FTP |
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-Related structure data
Related structure data | 1tfgS S: Starting model for refinement |
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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 NATIVE HOMODIMERIC FORM OF BMP-2 IS BUILT BY CRYSTALLOGRAPHIC SYMMETRY. THE MONOMERS ARE LINKED VIA A CYSTINE BRIDGE (CYS78 FROM BOTH SUBUNITS) |
-Components
#1: Protein | Mass: 12923.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12643 |
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#2: Chemical | ChemComp-MPD / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 Details: CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM 100 MM LITHIUM SULFATE, 12% TERT-BUTANOL, 50 MM CITRATE, PH 5.4 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Nov 30, 1997 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→10 Å / Num. obs: 4647 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 60.3 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 5.4 / % possible all: 82.2 |
Reflection shell | *PLUS % possible obs: 82.2 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TFG Resolution: 2.7→25 Å / Rfactor Rfree error: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.6 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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