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Yorodumi- PDB-2eqr: Solution structure of the first SANT domain from human nuclear re... -
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-Basic information
Entry | Database: PDB / ID: 2eqr | ||||||
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Title | Solution structure of the first SANT domain from human nuclear receptor corepressor 1 | ||||||
Components | Nuclear receptor corepressor 1 | ||||||
Keywords | TRANSCRIPTION / Sant domain / Nuclear receptor corepressor 1 / N-CoR1 / N-CoR / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / negative regulation of JNK cascade / negative regulation of glycolytic process / nuclear thyroid hormone receptor binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / locomotor rhythm ...NR1D1 (REV-ERBA) represses gene expression / Loss of MECP2 binding ability to the NCoR/SMRT complex / negative regulation of androgen receptor signaling pathway / negative regulation of JNK cascade / negative regulation of glycolytic process / nuclear thyroid hormone receptor binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of fatty acid metabolic process / Notch-HLH transcription pathway / locomotor rhythm / histone deacetylase complex / Regulation of MECP2 expression and activity / spindle assembly / Nuclear signaling by ERBB4 / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / negative regulation of miRNA transcription / HDACs deacetylate histones / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / mitotic spindle / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / HCMV Early Events / Nuclear Receptor transcription pathway / histone deacetylase binding / transcription corepressor activity / Circadian Clock / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Zhang, H.P. / Hayahsi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first SANT domain from human nuclear receptor corepressor 1 Authors: Zhang, H.P. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2eqr.cif.gz | 382.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eqr.ent.gz | 332.1 KB | Display | PDB format |
PDBx/mmJSON format | 2eqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/2eqr ftp://data.pdbj.org/pub/pdb/validation_reports/eq/2eqr | 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: 7172.054 Da / Num. of mol.: 1 / Fragment: Sant domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell-free protein synthesis / Gene: NCOR1 / Plasmid: P061225-49 / References: UniProt: O75376 |
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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: 1.14mM 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: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / 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 |