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Yorodumi- PDB-7v7w: Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex with o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7v7w | ||||||
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Title | Crystal Structure of the Heterodimeric HIF-3a:ARNT Complex with oleoylethanolamide (OEA) | ||||||
Components |
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Keywords | TRANSCRIPTION / Hypoxia-inducible factor | ||||||
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 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex ...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 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / positive regulation of protein sumoylation / Neddylation / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / cis-regulatory region sequence-specific DNA binding / 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 / cellular response to hypoxia / angiogenesis / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / nuclear body / protein dimerization activity / response to hypoxia / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / apoptotic process / protein-containing complex binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.507 Å | ||||||
Authors | Diao, X. / Ren, X. / Li, F.W. / Zhang, M. / Sun, X. / Wu, D. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Identification of oleoylethanolamide as an endogenous ligand for HIF-3 alpha. Authors: Diao, X. / Ye, F. / Zhang, M. / Ren, X. / Tian, X. / Lu, J. / Sun, X. / Hou, Z. / Chen, X. / Li, F. / Zhuang, J. / Ding, H. / Peng, C. / Rastinejad, F. / Luo, C. / Wu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v7w.cif.gz | 254.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v7w.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 7v7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v7w_validation.pdf.gz | 656.7 KB | Display | wwPDB validaton report |
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Full document | 7v7w_full_validation.pdf.gz | 666.5 KB | Display | |
Data in XML | 7v7w_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 7v7w_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v7/7v7w ftp://data.pdbj.org/pub/pdb/validation_reports/v7/7v7w | HTTPS FTP |
-Related structure data
Related structure data | 7v7lSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40683.133 Da / Num. of mol.: 1 / Fragment: Hydrocarbon receptor nuclear translocator 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 |
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#2: Protein | Mass: 40701.211 Da / Num. of mol.: 1 / Fragment: Hypoxia-inducible factor 3, HIF-3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hif3a / Plasmid: pSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q0VBL6 |
#3: Chemical | ChemComp-5YM / ( |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Sodium citrate tribasic dihydrate, 2-Propanol, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2019 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 28966 / % possible obs: 99.9 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.029 / Rrim(I) all: 0.095 / Χ2: 0.996 / Net I/σ(I): 6.7 / Num. measured all: 313133 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V7L Resolution: 2.507→35.929 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.45 / 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: 147.08 Å2 / Biso mean: 50.3906 Å2 / Biso min: 16.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.507→35.929 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 30.3161 Å / Origin y: 2.7462 Å / Origin z: 17.5073 Å
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Refinement TLS group |
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