[English] 日本語
Yorodumi- PDB-7xi4: Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xi4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the NPAS4-ARNT heterodimer in complex with DNA | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / protein-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 / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / negative regulation of inflammatory response / response to toxic substance / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to oxidative stress / sequence-specific DNA binding / transcription regulator complex / cell differentiation / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / protein heterodimerization activity / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of DNA-templated transcription / 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 / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.707 Å | ||||||
Authors | Sun, X.N. / Jing, L.Q. / Li, F.W. / Wu, D.L. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 Title: Structures of NPAS4-ARNT and NPAS4-ARNT2 heterodimers reveal new dimerization modalities in the bHLH-PAS transcription factor family. Authors: Sun, X. / Jing, L. / Li, F. / Zhang, M. / Diao, X. / Zhuang, J. / Rastinejad, F. / Wu, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7xi4.cif.gz | 151.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7xi4.ent.gz | 112.7 KB | Display | PDB format |
PDBx/mmJSON format | 7xi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xi4_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7xi4_full_validation.pdf.gz | 469.8 KB | Display | |
Data in XML | 7xi4_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 7xi4_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xi/7xi4 ftp://data.pdbj.org/pub/pdb/validation_reports/xi/7xi4 | HTTPS FTP |
-Related structure data
Related structure data | 7xhvC 7xi3C 4zpkS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 43306.199 Da / Num. of mol.: 1 / Fragment: ARNT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53762 |
---|---|
#2: Protein | Mass: 39381.828 Da / Num. of mol.: 1 / Fragment: NPAS4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Npas4 / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A1L327 |
#3: DNA chain | Mass: 5034.262 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#4: DNA chain | Mass: 4763.108 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.91 % / Mosaicity: 0.499 ° |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 8 / Details: ammonium tartrate dibasic, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: SIEMENS-NICOLET / Detector: PIXEL / Date: Jun 26, 2019 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4.7→50 Å / Num. obs: 6762 / % possible obs: 99.9 % / Redundancy: 23.3 % / Biso Wilson estimate: 57.49 Å2 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.054 / Rrim(I) all: 0.267 / Χ2: 0.977 / Net I/σ(I): 2.4 / Num. measured all: 157818 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZPK Resolution: 4.707→29.63 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.71 / Stereochemistry target values: ML
| ||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||
Displacement parameters | Biso max: 270.74 Å2 / Biso mean: 109.9629 Å2 / Biso min: 30 Å2 | ||||||||||||||||||
Refinement step | Cycle: final / Resolution: 4.707→29.63 Å
| ||||||||||||||||||
LS refinement shell | Resolution: 4.707→4.78 Å / Rfactor Rfree error: 0
|