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Yorodumi- PDB-5sy7: Crystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5sy7 | ||||||
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Title | Crystal Structure of the Heterodimeric NPAS3-ARNT Complex with HRE DNA | ||||||
Components |
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Keywords | transcription/DNA / bHLH-PAS protein / transcription factor / heterodimeric complex / transcription-DNA complex | ||||||
Function / homology | Function and homology information Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation ...Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / maternal behavior / startle response / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / locomotory behavior / RNA polymerase II transcription regulatory region sequence-specific DNA binding / response to toxic substance / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / cell differentiation / response to hypoxia / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.2 Å | ||||||
Authors | Wu, D. / Su, X. / Potluri, N. / Kim, Y. / Rastinejad, F. | ||||||
Citation | Journal: Elife / Year: 2016 Title: NPAS1-ARNT and NPAS3-ARNT crystal structures implicate the bHLH-PAS family as multi-ligand binding transcription factors. Authors: Wu, D. / Su, X. / Potluri, N. / Kim, Y. / Rastinejad, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5sy7.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5sy7.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 5sy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/5sy7 ftp://data.pdbj.org/pub/pdb/validation_reports/sy/5sy7 | HTTPS FTP |
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-Related structure data
Related structure data | 5sy5C 4zpkS S: Starting model for refinement C: citing same article (ref.) |
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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: Protein | Mass: 43437.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53762 |
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#2: Protein | Mass: 46225.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas3, Mop6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9QZQ0 |
#3: DNA chain | Mass: 6527.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA sense strand / Source: (synth.) Mus musculus (house mouse) |
#4: DNA chain | Mass: 6363.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA antisense strand / Source: (synth.) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM NH4F, 9% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.2→50 Å / Num. obs: 7195 / % possible obs: 94.6 % / Redundancy: 5.2 % / Biso Wilson estimate: 37.41 Å2 / Rmerge(I) obs: 0.06 / Net I/av σ(I): 20.01 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZPK Resolution: 4.2→45.842 Å / SU ML: 0.78 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 220.01 Å2 / Biso mean: 66.8626 Å2 / Biso min: 5.11 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.2→45.842 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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