+Open data
-Basic information
Entry | Database: PDB / ID: 8e3g | |||||||||
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Title | BMP2/GDF5 heterodimer | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Cystine-knot Growth factor Heterodimer | |||||||||
Function / homology | Function and homology information ossification involved in bone remodeling / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly 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 ...ossification involved in bone remodeling / cardiac atrium formation / cardiocyte differentiation / negative regulation of calcium-independent cell-cell adhesion / cardiac jelly 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 / negative regulation of steroid biosynthetic process / ameloblast differentiation / positive regulation of extracellular matrix constituent secretion / forelimb morphogenesis / 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 / BMP binding / chondroblast differentiation / positive regulation of phosphatase activity / hindlimb morphogenesis / positive regulation of cartilage development / proteoglycan metabolic process / heart induction / positive regulation of peroxisome proliferator activated receptor signaling pathway / negative regulation of mesenchymal cell apoptotic process / pericardium development / lung vasculature development / positive regulation of chondrocyte differentiation / mesenchymal cell apoptotic process / 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 / positive regulation of BMP signaling pathway / positive regulation of ossification / astrocyte differentiation / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / 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 / regulation of multicellular organism growth / positive regulation of Wnt signaling pathway / positive regulation of fat cell differentiation / epithelial to mesenchymal transition / cell fate commitment / chondrocyte differentiation / positive regulation of bone mineralization / BMP signaling pathway / positive regulation of osteoblast differentiation / positive regulation of epithelial to mesenchymal transition / response to mechanical stimulus / Notch signaling pathway / positive regulation of neuron differentiation / protein serine/threonine kinase activator activity / osteoclast differentiation / transforming growth factor beta receptor signaling pathway / negative regulation of MAP kinase activity / skeletal system development / cytokine activity / negative regulation of smooth muscle cell proliferation / animal organ morphogenesis / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Gipson, G.R. / Nolan, K.T. / Thompson, T.B. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Bmc Biol. / Year: 2023 Title: Formation and characterization of BMP2/GDF5 and BMP4/GDF5 heterodimers. Authors: Gipson, G.R. / Nolan, K. / Kattamuri, C. / Kenny, A.P. / Agricola, Z. / Edwards, N.A. / Zinski, J. / Czepnik, M. / Mullins, M.C. / Zorn, A.M. / Thompson, T.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8e3g.cif.gz | 297.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8e3g.ent.gz | 204.2 KB | Display | PDB format |
PDBx/mmJSON format | 8e3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8e3g_validation.pdf.gz | 466.5 KB | Display | wwPDB validaton report |
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Full document | 8e3g_full_validation.pdf.gz | 469.4 KB | Display | |
Data in XML | 8e3g_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 8e3g_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/8e3g ftp://data.pdbj.org/pub/pdb/validation_reports/e3/8e3g | HTTPS FTP |
-Related structure data
Related structure data | 1reuS 1waqS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 12923.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2, BMP2A / Production host: Escherichia coli (E. coli) / References: UniProt: P12643 #2: Protein | Mass: 13598.638 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43026 #3: Chemical | ChemComp-GOL / Has ligand of interest | N | |
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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: 4.6 Å3/Da / Density % sol: 73.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris, magnesium formate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→76.6 Å / Num. obs: 24734 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 56.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.055 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.363 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2428 / CC1/2: 0.709 / Rpim(I) all: 0.426 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WAQ, 1REU Resolution: 2.8→76.55 Å / SU ML: 0.3555 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.5825 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.68 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→76.55 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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