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Yorodumi- PDB-6hil: X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtyp... -
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-Basic information
Entry | Database: PDB / ID: 6hil | ||||||
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Title | X-ray structure of TEAD1(Y421H mutant) complexed with YAP(wildtype): Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy | ||||||
Components |
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Keywords | TRANSCRIPTION / OTHER / TRANSCRIPTION FACTOR | ||||||
Function / homology | Function and homology information enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / contact inhibition / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching / polarized epithelial cell differentiation / notochord development / negative regulation of cilium assembly / lung epithelial cell differentiation / YAP1- and WWTR1 (TAZ)-stimulated gene expression / heart process / trophectodermal cell differentiation / paraxial mesoderm development / tissue homeostasis / hippo signaling / regulation of stem cell proliferation / EGR2 and SOX10-mediated initiation of Schwann cell myelination / intestinal epithelial cell development / negative regulation of epithelial cell apoptotic process / Formation of axial mesoderm / negative regulation of stem cell differentiation / embryonic heart tube morphogenesis / female germ cell nucleus / proline-rich region binding / Signaling by Hippo / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of epithelial cell differentiation / negative regulation of fat cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / RUNX2 regulates osteoblast differentiation / progesterone receptor signaling pathway / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / positive regulation of osteoblast differentiation / embryonic organ development / vasculogenesis / Nuclear signaling by ERBB4 / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / response to progesterone / epithelial cell proliferation / positive regulation of epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / cellular response to gamma radiation / wound healing / cell morphogenesis / positive regulation of miRNA transcription / positive regulation of protein localization to nucleus / positive regulation of canonical Wnt signaling pathway / transcription corepressor activity / cell-cell junction / sequence-specific double-stranded DNA binding / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / transcription coactivator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / DNA damage response / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Kallen, J. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Molecular and structural characterization of a TEAD mutation at the origin of Sveinsson's chorioretinal atrophy. Authors: Bokhovchuk, F. / Mesrouze, Y. / Izaac, A. / Meyerhofer, M. / Zimmermann, C. / Fontana, P. / Schmelzle, T. / Erdmann, D. / Furet, P. / Kallen, J. / Chene, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hil.cif.gz | 207.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hil.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 6hil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hil ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hil | HTTPS FTP |
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-Related structure data
Related structure data | 6hikC 3kysS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25223.740 Da / Num. of mol.: 4 / Fragment: C-terminal domain, YAP binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / References: UniProt: P28347 #2: Protein/peptide | Mass: 4650.309 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46937 #3: Chemical | ChemComp-MYR / #4: 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: 2.1 Å3/Da / Density % sol: 41.4 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 22% (w/v) PEG3350, 0.2M Na Malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2018 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.9 Å / Num. obs: 41611 / % possible obs: 95.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 51.3 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.0998 / Rrim(I) all: 0.065 / Net I/σ(I): 10.9 / Num. measured all: 74068 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.2 / Rpim(I) all: 0.702 / Rrim(I) all: 0.804 / % possible all: 95.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KYS Resolution: 2.3→19.9 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.755 / SU ML: 0.25 / SU R Cruickshank DPI: 0.5941 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.594 / ESU R Free: 0.286 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 133.82 Å2 / Biso mean: 48.846 Å2 / Biso min: 19.82 Å2
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Refinement step | Cycle: final / Resolution: 2.3→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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