+Open data
-Basic information
Entry | Database: PDB / ID: 1a6y | ||||||
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Title | REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX | ||||||
Components |
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Keywords | TRANSCRIPTION/DNA / ORPHAN RECEPTOR / NUCLEAR RECEPTOR / DNA-BINDING / REVERB / REV-ERB / TRANSCRIPTION REGULATION / TRANSCRIPTION-DNA COMPLEX | ||||||
Function / homology | Function and homology information regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / response to leptin / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway ...regulation of circadian sleep/wake cycle / positive regulation of bile acid biosynthetic process / NR1D1 (REV-ERBA) represses gene expression / circadian temperature homeostasis / regulation of type B pancreatic cell proliferation / negative regulation of astrocyte activation / negative regulation of microglial cell activation / response to leptin / negative regulation of neuroinflammatory response / negative regulation of toll-like receptor 4 signaling pathway / regulation of insulin secretion involved in cellular response to glucose stimulus / E-box binding / glycogen biosynthetic process / negative regulation of cold-induced thermogenesis / regulation of fat cell differentiation / nuclear steroid receptor activity / intracellular glucose homeostasis / regulation of lipid metabolic process / cellular response to interleukin-1 / proteasomal protein catabolic process / hormone-mediated signaling pathway / negative regulation of canonical NF-kappaB signal transduction / transcription corepressor binding / cholesterol homeostasis / regulation of circadian rhythm / RNA polymerase II transcription regulatory region sequence-specific DNA binding / PPARA activates gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / circadian regulation of gene expression / Heme signaling / protein destabilization / Nuclear Receptor transcription pathway / Transcriptional activation of mitochondrial biogenesis / nuclear receptor activity / sequence-specific double-stranded DNA binding / Circadian Clock / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / transcription cis-regulatory region binding / dendritic spine / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / dendrite / heme binding / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Zhao, Q. / Khorasanizadeh, S. / Rastinejad, F. | ||||||
Citation | Journal: Mol.Cell / Year: 1998 Title: Structural elements of an orphan nuclear receptor-DNA complex. Authors: Zhao, Q. / Khorasanizadeh, S. / Miyoshi, Y. / Lazar, M.A. / Rastinejad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a6y.cif.gz | 71.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a6y.ent.gz | 52.5 KB | Display | PDB format |
PDBx/mmJSON format | 1a6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a6y_validation.pdf.gz | 455.2 KB | Display | wwPDB validaton report |
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Full document | 1a6y_full_validation.pdf.gz | 473.2 KB | Display | |
Data in XML | 1a6y_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 1a6y_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/1a6y ftp://data.pdbj.org/pub/pdb/validation_reports/a6/1a6y | HTTPS FTP |
-Related structure data
Related structure data | 2nllS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6254.863 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: DNA chain | Mass: 6124.965 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Protein | Mass: 10902.009 Da / Num. of mol.: 2 Fragment: DNA BINDING DOMAIN CONSISTS OF RESIDUES A 101 TO A 164, B 101 TO B 164 Mutation: H116L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P20393 #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 53.4 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: PROTEIN AND DNA COMPLEX WAS CRYSTALLIZED FROM 25-30% PEG 8000, 5 MM MGCL2, 400 MM NACL2, 100 MM TRIS, PH 7.5., VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Details: Zhao, Q., (1998) Mol. Cell, 1, 849. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: NONE |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→19.4 Å / Num. obs: 13482 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.088 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 2.3→2.38 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.492 / % possible all: 94 |
Reflection | *PLUS Rmerge(I) obs: 0.088 |
Reflection shell | *PLUS % possible obs: 94 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2NLL (TR PORTION) Resolution: 2.3→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: THERE IS AN INSERT GLN 133A IN BOTH CHAIN A AND B
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Displacement parameters | Biso mean: 31.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.1921 / Rfactor Rfree: 0.2882 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.313 |