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- PDB-6wmq: Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-B... -
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Basic information
Entry | Database: PDB / ID: 6wmq | ||||||
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Title | Crystal Structure of Human REV-ERBbeta Ligand Binding Domain Co-Bound to Heme and NCoR ID1 Peptide | ||||||
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![]() | TRANSCRIPTION / Nuclear receptor / heme-binding protein | ||||||
Function / homology | ![]() regulation of skeletal muscle cell differentiation / 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 / circadian behavior / nuclear thyroid hormone receptor binding / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis ...regulation of skeletal muscle cell differentiation / 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 / circadian behavior / nuclear thyroid hormone receptor binding / negative regulation of fatty acid metabolic process / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / Notch-HLH transcription pathway / locomotor rhythm / lipid homeostasis / histone deacetylase complex / Regulation of MECP2 expression and activity / regulation of lipid metabolic process / spindle assembly / Nuclear signaling by ERBB4 / energy homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / transcription repressor complex / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / negative regulation of miRNA transcription / nuclear receptor binding / HDACs deacetylate histones / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Heme signaling / Transcriptional activation of mitochondrial biogenesis / regulation of circadian rhythm / PPARA activates gene expression / Cytoprotection by HMOX1 / NOTCH1 Intracellular Domain Regulates Transcription / mitotic spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / transcription corepressor activity / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / chromatin organization / regulation of inflammatory response / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mosure, S.A. / Shang, J. / Kojetin, D.J. | ||||||
![]() | ![]() Title: Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERB beta. Authors: Mosure, S.A. / Strutzenberg, T.S. / Shang, J. / Munoz-Tello, P. / Solt, L.A. / Griffin, P.R. / Kojetin, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 101.6 KB | Display | ![]() |
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PDB format | ![]() | 75.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wmsC ![]() 3cqvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22494.861 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 2741.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 2.0 M ammonium sulfate, 0.1 M Na HEPES, pH 7.5, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97741 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→54 Å / Num. obs: 14814 / % possible obs: 99.91 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.83 |
Reflection shell | Resolution: 2.55→2.64 Å / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 2.26 / Num. unique obs: 14814 / CC1/2: 0.727 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CQV Resolution: 2.55→53.154 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.25 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.54 Å2 / Biso mean: 30.4957 Å2 / Biso min: 8.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.55→53.154 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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