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Yorodumi- PDB-2yt5: Solution structure of the PHD domain of Metal-response element-bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yt5 | ||||||
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Title | Solution structure of the PHD domain of Metal-response element-binding transcription factor 2 | ||||||
Components | Metal-response element-binding transcription factor 2 | ||||||
Keywords | TRANSCRIPTION / PHD domain / Metal-response element-binding transcription factor 2 / Zinc-regulated factor 1 / ZiRF1 / Metal-response element DNA-binding protein M96 / Metal-regulatory transcription factor 2 / PCL2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information PRC2 methylates histones and DNA / segment specification / stem cell population maintenance / negative regulation of gene expression, epigenetic / methylated histone binding / epigenetic regulation of gene expression / transcription corepressor binding / cellular response to leukemia inhibitory factor / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...PRC2 methylates histones and DNA / segment specification / stem cell population maintenance / negative regulation of gene expression, epigenetic / methylated histone binding / epigenetic regulation of gene expression / transcription corepressor binding / cellular response to leukemia inhibitory factor / stem cell differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / chromatin binding / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Masuda, K. / Muto, Y. / Isono, K. / Watanabe, S. / Harada, T. / Kigawa, T. / Koseki, H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the PHD domain of Metal-response element-binding transcription factor 2 Authors: Masuda, K. / Muto, Y. / Isono, K. / Watanabe, S. / Harada, T. / Kigawa, T. / Koseki, H. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yt5.cif.gz | 381.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yt5.ent.gz | 315.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yt5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yt5_validation.pdf.gz | 343.3 KB | Display | wwPDB validaton report |
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Full document | 2yt5_full_validation.pdf.gz | 468.1 KB | Display | |
Data in XML | 2yt5_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2yt5_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2yt5 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2yt5 | 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: 7279.103 Da / Num. of mol.: 1 / Fragment: PHD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Mtf2 / Plasmid: P061010-06 / References: UniProt: Q02395 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |