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Yorodumi- PDB-2hzd: NMR structure of the DNA-binding TEA domain and insights into TEF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hzd | ||||||
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Title | NMR structure of the DNA-binding TEA domain and insights into TEF-1 function | ||||||
Components | Transcriptional enhancer factor TEF-1 | ||||||
Keywords | GENE REGULATION / DNA-BINDING / HELIX-TURN-HELIX | ||||||
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 | SOLUTION NMR / torsion angle dynamics, simulated annealing | ||||||
Authors | Anbanandam, A. / Veeraraghavan, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006 Title: Insights into transcription enhancer factor 1 (TEF-1) activity from the solution structure of the TEA domain. Authors: Anbanandam, A. / Albarado, D.C. / Nguyen, C.T. / Halder, G. / Gao, X. / Veeraraghavan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hzd.cif.gz | 656.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hzd.ent.gz | 552.8 KB | Display | PDB format |
PDBx/mmJSON format | 2hzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hzd_validation.pdf.gz | 341.6 KB | Display | wwPDB validaton report |
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Full document | 2hzd_full_validation.pdf.gz | 526.4 KB | Display | |
Data in XML | 2hzd_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 2hzd_validation.cif.gz | 54.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/2hzd ftp://data.pdbj.org/pub/pdb/validation_reports/hz/2hzd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 9548.997 Da / Num. of mol.: 1 / Fragment: N-TERMINAL TEA DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TEAD1, TCF13, TEF1 / Plasmid: PET21D / Production host: Escherichia coli (E. coli) / References: UniProt: P28347 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: 3D TRIPLE RESONANCE EXPERIMENTS |
-Sample preparation
Details | Contents: 1.3 mM TEA U-15N, 13C, 100 mM phosphate buffer, 95% H2O, 5% D2O Solvent system: 100 mM phosphate buffer, 95% H2O, 5% D2O |
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Sample conditions | Ionic strength: 100 mM NaCl / pH: 5.85 / Pressure: 1 atm / Temperature: 285 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software | Name: CNS / Version: 1.1 / Developer: BRUNGER / Classification: refinement |
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Refinement | Method: torsion angle dynamics, simulated annealing / Software ordinal: 1 |
NMR representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 25 |