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Yorodumi- PDB-7oyj: Crystal structure of hTEAD2 in complex with fragment at the inter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oyj | ||||||
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Title | Crystal structure of hTEAD2 in complex with fragment at the interface 2 | ||||||
Components | Transcriptional enhancer factor TEF-4 | ||||||
Keywords | TRANSCRIPTION / TEAD / Fragment | ||||||
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 / sequence-specific double-stranded DNA binding / disordered domain specific binding / protein-containing complex assembly / transcription regulator complex / 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 DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive 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: 1.91 Å | ||||||
Authors | Guichou, J.F. / Gelin, M. / Allemand, F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2022 Title: Toward the Design of Ligands Selective for the C-Terminal Domain of TEADs. Authors: Liberelle, M. / Toulotte, F. / Renault, N. / Gelin, M. / Allemand, F. / Melnyk, P. / Guichou, J.F. / Cotelle, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oyj.cif.gz | 181.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oyj.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 7oyj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oyj_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7oyj_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7oyj_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 7oyj_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/7oyj ftp://data.pdbj.org/pub/pdb/validation_reports/oy/7oyj | HTTPS FTP |
-Related structure data
Related structure data | 5dq8S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27489.096 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-3DI / | #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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 18, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.965459 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.592→74.786 Å / Num. obs: 65881 / % possible obs: 91.8 % / Redundancy: 2.4 % / Biso Wilson estimate: 36.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.025 / Rrim(I) all: 0.042 / Net I/σ(I): 14.8 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DQ8 Resolution: 1.91→53.04 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.49 / Stereochemistry target values: ML
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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: 120.39 Å2 / Biso mean: 53.448 Å2 / Biso min: 27.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.91→53.04 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23
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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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