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Yorodumi- PDB-6hik: X-ray structure of TEAD4(Y429H) mutant) complexed with YAP (wildt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hik | ||||||
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Title | X-ray structure of TEAD4(Y429H) 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 | ||||||
Function / homology | Function and homology information trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / glandular epithelial cell differentiation / TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / bud elongation involved in lung branching ...trophectodermal cell fate commitment / enterocyte differentiation / regulation of keratinocyte proliferation / regulation of metanephric nephron tubule epithelial cell differentiation / cardiac muscle tissue regeneration / 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 / regulation of stem cell proliferation / hippo signaling / tissue homeostasis / 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 / cell fate specification / muscle organ development / negative regulation of epithelial cell differentiation / organ growth / positive regulation of stem cell population maintenance / interleukin-6-mediated signaling pathway / positive regulation of Notch signaling pathway / negative regulation of fat cell differentiation / RUNX2 regulates osteoblast differentiation / Zygotic genome activation (ZGA) / somatic stem cell population maintenance / regulation of neurogenesis / canonical Wnt signaling pathway / vasculogenesis / embryonic organ development / positive regulation of osteoblast differentiation / cellular response to retinoic acid / extrinsic apoptotic signaling pathway / Nuclear signaling by ERBB4 / keratinocyte differentiation / positive regulation of cardiac muscle cell proliferation / embryo implantation / epithelial cell proliferation / skeletal system development / positive regulation of epithelial cell proliferation / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cell morphogenesis / cellular response to gamma radiation / positive regulation of protein localization to nucleus / transcription corepressor activity / cell-cell junction / positive regulation of canonical Wnt signaling pathway / cell junction / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / 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-templated transcription / DNA damage response / chromatin binding / positive regulation of gene expression / chromatin / 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 / nucleoplasm / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 | 6hik.cif.gz | 74.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hik.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 6hik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hik_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 6hik_full_validation.pdf.gz | 454.3 KB | Display | |
Data in XML | 6hik_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6hik_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/6hik ftp://data.pdbj.org/pub/pdb/validation_reports/hi/6hik | HTTPS FTP |
-Related structure data
Related structure data | 6hilC 6ge3S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25475.693 Da / Num. of mol.: 1 / Fragment: C-terminal domain, YAP binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD4, RTEF1, TCF13L1, TEF3 / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15561 | ||
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#2: Protein/peptide | Mass: 4547.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P46937 | ||
#3: Chemical | ChemComp-MYR / | ||
#4: Chemical | #5: 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: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 1.4M Na/K PO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99981 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2018 |
Radiation | Monochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99981 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→19.95 Å / Num. obs: 34599 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.083 / Net I/σ(I): 21 / Num. measured all: 449159 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 13.5 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.6 / Rpim(I) all: 0.88 / Rrim(I) all: 1.05 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GE3 Resolution: 1.65→19.95 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.037 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.107 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: 52.58 Å2 / Biso mean: 23.128 Å2 / Biso min: 11.51 Å2
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Refinement step | Cycle: final / Resolution: 1.65→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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