+Open data
-Basic information
Entry | Database: PDB / ID: 7tyu | ||||||
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Title | TEAD2 bound to Compound 2 | ||||||
Components | Transcriptional enhancer factor TEF-4 | ||||||
Keywords | TRANSCRIPTION / Small molecule PPI inhibitor complex | ||||||
Function / homology | Function and homology information TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis ...TEAD-YAP complex / lateral mesoderm development / RUNX3 regulates YAP1-mediated transcription / notochord development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / paraxial mesoderm development / hippo signaling / regulation of stem cell differentiation / Formation of axial mesoderm / embryonic heart tube morphogenesis / vasculogenesis / embryonic organ development / cellular response to retinoic acid / neural tube closure / transcription coactivator binding / disordered domain specific binding / sequence-specific double-stranded DNA binding / transcription regulator complex / protein-containing complex assembly / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Noland, C.L. / Fong, R. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Novel mechanism of YAP-TEAD inhibition results in targeted chromatin remodeling and reveals an expanded Hippo dependent landscape in cancers Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / ...Authors: Hagenbeek, T.J. / Zbieg, J.R. / Noland, C.L. / Yao, X. / Schmidt, S. / Clausen, S. / Steffek, M. / Lee, W. / Beroza, P. / Martin, S. / Lin, E. / Fong, R. / Di Lello, P. / Kubala, M.H. / Lacap, J.A. / Yang, M.N.Y. / Maddalo, D. / Lau, J.T. / An, L. / Levy, E. / Lorenzo, M.N. / Lee, H.J. / Pham, T.H. / Modrusan, Z. / Zang, R. / Chen, Y.C. / Li, J. / Hafner, M. / Chang, M.T. / Crawford, J.J. / Dey, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tyu.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tyu.ent.gz | 144.7 KB | Display | PDB format |
PDBx/mmJSON format | 7tyu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/7tyu ftp://data.pdbj.org/pub/pdb/validation_reports/ty/7tyu | HTTPS FTP |
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-Related structure data
Related structure data | 7typC 7tyqC 5emvS S: Starting model for refinement C: citing same article (ref.) |
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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: 26300.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD2, TEF4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15562 #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M Na/K Tartrate, 0.1 M Bis Tris pH 6.5, 35% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→53.835 Å / Num. obs: 31238 / % possible obs: 92.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.55 Å2 / CC1/2: 1 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.784→1.986 Å / Num. unique obs: 1536 / CC1/2: 0.783 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EMV Resolution: 1.78→33.35 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.5516 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: 51.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→33.35 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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