+Open data
-Basic information
Entry | Database: PDB / ID: 2cob | ||||||
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Title | Solution structures of the HTH domain of human LCoR protein | ||||||
Components | LCoR protein | ||||||
Keywords | DNA BINDING PROTEIN / MLR2 / KIAA1795 / helix-turn-helix / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information transcription corepressor binding => GO:0001222 / histone methyltransferase binding / ubiquitin-specific protease binding / cellular response to estradiol stimulus / nuclear estrogen receptor binding / histone deacetylase binding / transcription corepressor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II ...transcription corepressor binding => GO:0001222 / histone methyltransferase binding / ubiquitin-specific protease binding / cellular response to estradiol stimulus / nuclear estrogen receptor binding / histone deacetylase binding / transcription corepressor activity / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / negative 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, restrained molecular dynamics | ||||||
Authors | Nameki, N. / Umehara, T. / Sato, M. / Koshiba, S. / Inoue, M. / Tanaka, A. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structures of the HTH domain of human LCoR protein Authors: Nameki, N. / Umehara, T. / Sato, M. / Koshiba, S. / Inoue, M. / Tanaka, A. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cob.cif.gz | 430.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cob.ent.gz | 376.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cob.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/2cob ftp://data.pdbj.org/pub/pdb/validation_reports/co/2cob | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7820.126 Da / Num. of mol.: 1 / Fragment: HTH domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: MLR2 / Plasmid: P040816-15 / References: UniProt: Q5VW16, UniProt: Q96JN0*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM HTH domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 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, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function,structures with the lowest energy,structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |