+Open data
-Basic information
Entry | Database: PDB / ID: 5xod | |||||||||
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Title | Crystal structure of human Smad2-Ski complex | |||||||||
Components |
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Keywords | TRANSCRIPTION / transcription factor / complex | |||||||||
Function / homology | Function and homology information nose morphogenesis / histone deacetylase inhibitor activity / zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway ...nose morphogenesis / histone deacetylase inhibitor activity / zygotic specification of dorsal/ventral axis / regulation of binding / homomeric SMAD protein complex / paraxial mesoderm morphogenesis / activin responsive factor complex / SMAD4 MH2 Domain Mutants in Cancer / SMAD2/3 MH2 Domain Mutants in Cancer / nodal signaling pathway / SMAD protein complex / myotube differentiation / endoderm formation / co-SMAD binding / heteromeric SMAD protein complex / determination of left/right asymmetry in lateral mesoderm / odontoblast differentiation / secondary palate development / pericardium development / FOXO-mediated transcription of cell cycle genes / lens morphogenesis in camera-type eye / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / negative regulation of Schwann cell proliferation / Transcriptional regulation of pluripotent stem cells / regulation of transforming growth factor beta receptor signaling pathway / embryonic foregut morphogenesis / transforming growth factor beta receptor binding / primary miRNA processing / camera-type eye morphogenesis / Germ layer formation at gastrulation / olfactory bulb development / pulmonary valve morphogenesis / Signaling by BMP / myelination in peripheral nervous system / type I transforming growth factor beta receptor binding / Formation of definitive endoderm / activin receptor signaling pathway / signal transduction involved in regulation of gene expression / Signaling by Activin / negative regulation of activin receptor signaling pathway / SMAD protein signal transduction / Formation of axial mesoderm / positive regulation of BMP signaling pathway / Signaling by NODAL / camera-type eye development / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / aortic valve morphogenesis / pancreas development / bone morphogenesis / insulin secretion / embryonic limb morphogenesis / face morphogenesis / anterior/posterior axis specification / anterior/posterior pattern specification / cardiac muscle cell proliferation / ureteric bud development / endocardial cushion morphogenesis / organ growth / adrenal gland development / negative regulation of SMAD protein signal transduction / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / somatic stem cell population maintenance / R-SMAD binding / mesoderm formation / negative regulation of BMP signaling pathway / positive regulation of Wnt signaling pathway / anatomical structure morphogenesis / phosphatase binding / negative regulation of osteoblast differentiation / cell fate commitment / positive regulation of DNA binding / cis-regulatory region sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / skeletal muscle fiber development / positive regulation of epithelial to mesenchymal transition / gastrulation / negative regulation of fibroblast proliferation / transcription repressor complex / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / post-embryonic development / neural tube closure / cell motility / cellular response to glucose stimulus / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / lung development / tau protein binding / PML body / DNA-binding transcription repressor activity, RNA polymerase II-specific / disordered domain specific binding / retina development in camera-type eye / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | |||||||||
Authors | Miyazono, K. / Moriwaki, S. / Ito, T. / Tanokura, M. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Signal / Year: 2018 Title: Hydrophobic patches on SMAD2 and SMAD3 determine selective binding to cofactors Authors: Miyazono, K.I. / Moriwaki, S. / Ito, T. / Kurisaki, A. / Asashima, M. / Tanokura, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xod.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xod.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xod ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xod | HTTPS FTP |
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-Related structure data
Related structure data | 5xocC 1mjsS 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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-Components
#1: Protein | Mass: 22461.432 Da / Num. of mol.: 1 / Fragment: UNP residues 262-458 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SMAD2, MADH2, MADR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15796 |
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#2: Protein/peptide | Mass: 3167.418 Da / Num. of mol.: 1 / Fragment: UNP residues 15-40 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SKI / Production host: Escherichia coli (E. coli) / References: UniProt: P12755 |
#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: 2.21 Å3/Da / Density % sol: 44.44 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M sodium acetate tri-hydrate pH 4.6 and 1.85 M sodium formate |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: CCD / Date: Nov 2, 2015 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→45.25 Å / Num. obs: 37448 / % possible obs: 99.8 % / Redundancy: 9.3 % / Biso Wilson estimate: 31.92 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.012 / Rrim(I) all: 0.037 / Net I/σ(I): 28 / Num. measured all: 180013 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MJS Resolution: 1.851→45.25 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 28.16 / Stereochemistry target values: ML Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
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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 max: 126.73 Å2 / Biso mean: 60.5615 Å2 / Biso min: 24.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.851→45.25 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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