+Open data
-Basic information
Entry | Database: PDB / ID: 5nnx | ||||||
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Title | TEAD1 bound to DNA | ||||||
Components |
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Keywords | TRANSCRIPTION / Transcription factor / DNA binding | ||||||
Function / homology | Function and homology information TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly ...TEAD-YAP complex / RUNX3 regulates YAP1-mediated transcription / YAP1- and WWTR1 (TAZ)-stimulated gene expression / hippo signaling / EGR2 and SOX10-mediated initiation of Schwann cell myelination / embryonic organ development / positive regulation of miRNA transcription / sequence-specific double-stranded DNA binding / positive regulation of cell growth / protein-containing complex assembly / transcription regulator complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.29 Å | ||||||
Authors | Morgunova, E. / Jolma, A. / Yin, Y. / Popov, A. / Taipale, J. | ||||||
Citation | Journal: To Be Published Title: TEAD1 bound to DNA Authors: Morgunova, E. / Jolma, A. / Yin, Y. / Popov, A. / Taipale, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nnx.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nnx.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 5nnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/5nnx ftp://data.pdbj.org/pub/pdb/validation_reports/nn/5nnx | HTTPS FTP |
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-Related structure data
Related structure data | 4z8eS S: Starting model for refinement |
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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: DNA chain | Mass: 5411.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#2: DNA chain | Mass: 5620.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#3: Protein | Mass: 8590.927 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: pETG20A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P28347 |
#4: 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: 4.87 Å3/Da / Density % sol: 74.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.24 / Details: Ammonium Sulphate, MOPS, PEG (6000), PME(550) |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2016 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 3.29→46.46 Å / Num. obs: 5806 / % possible obs: 97.4 % / Redundancy: 5.9 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.035 / Rrim(I) all: 0.087 / Net I/σ(I): 9.8 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z8E Resolution: 3.29→46 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.935 / SU B: 31.03 / SU ML: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.496 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 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: 319.03 Å2 / Biso mean: 167.303 Å2 / Biso min: 86.11 Å2
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Refinement step | Cycle: final / Resolution: 3.29→46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.289→3.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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