+Open data
-Basic information
Entry | Database: PDB / ID: 6omo | |||||||||
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Title | Human BMP6 homodimer | |||||||||
Components | Bone morphogenetic protein 6 | |||||||||
Keywords | CYTOKINE / BMP / bone morphogenetic protein | |||||||||
Function / homology | Function and homology information positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / BMP receptor binding / type B pancreatic cell development / eye development / positive regulation of lipopolysaccharide-mediated signaling pathway / male genitalia development ...positive regulation of aldosterone biosynthetic process / positive regulation of aldosterone secretion / negative regulation of adherens junction organization / positive regulation of chondrocyte differentiation / positive regulation of endothelial cell differentiation / BMP receptor binding / type B pancreatic cell development / eye development / positive regulation of lipopolysaccharide-mediated signaling pathway / male genitalia development / negative regulation of cell-cell adhesion mediated by cadherin / cellular response to BMP stimulus / endochondral ossification / positive regulation of vascular permeability / cartilage development / positive regulation of SMAD protein signal transduction / response to magnesium ion / positive regulation of osteoblast differentiation / BMP signaling pathway / positive regulation of bone mineralization / response to retinoic acid / response to glucocorticoid / positive regulation of neuron differentiation / positive regulation of endothelial cell proliferation / response to activity / kidney development / skeletal system development / cytokine activity / positive regulation of epithelial cell proliferation / positive regulation of protein secretion / growth factor activity / bone development / neuron differentiation / cellular response to iron ion / osteoblast differentiation / multicellular organismal-level iron ion homeostasis / cellular response to mechanical stimulus / positive regulation of peptidyl-tyrosine phosphorylation / intracellular iron ion homeostasis / vesicle / immune response / inflammatory response / protein heterodimerization activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Juo, Z.S. / Seeherman, H. | |||||||||
Citation | Journal: Sci Transl Med / Year: 2019 Title: A BMP/activin A chimera is superior to native BMPs and induces bone repair in nonhuman primates when delivered in a composite matrix. Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / ...Authors: Seeherman, H.J. / Berasi, S.P. / Brown, C.T. / Martinez, R.X. / Juo, Z.S. / Jelinsky, S. / Cain, M.J. / Grode, J. / Tumelty, K.E. / Bohner, M. / Grinberg, O. / Orr, N. / Shoseyov, O. / Eyckmans, J. / Chen, C. / Morales, P.R. / Wilson, C.G. / Vanderploeg, E.J. / Wozney, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6omo.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6omo.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 6omo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/6omo ftp://data.pdbj.org/pub/pdb/validation_reports/om/6omo | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules IJ
#1: Protein | Mass: 11776.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BMP6, VGR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22004 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 47 molecules
#3: Chemical | ChemComp-IPA / #5: Chemical | #6: 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: 4.89 Å3/Da / Density % sol: 74.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris HCl 8.0, 15% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MAC Science DIP-320 / Detector: IMAGE PLATE / Date: Dec 16, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.7 Å / Num. obs: 14720 / % possible obs: 99.49 % / Redundancy: 4 % / Biso Wilson estimate: 79.1 Å2 / Net I/σ(I): 8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→48.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9226 / SU R Cruickshank DPI: 0.268 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.271 / SU Rfree Blow DPI: 0.219 / SU Rfree Cruickshank DPI: 0.219
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Displacement parameters | Biso mean: 68.24 Å2
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Refine analyze | Luzzati coordinate error obs: 0.344 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.8→48.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.81 Å / Total num. of bins used: 7
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