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Yorodumi- PDB-6e3s: Crystal Structure of the Heterodimeric HIF-2 Complex with Antagon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e3s | |||||||||
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Title | Crystal Structure of the Heterodimeric HIF-2 Complex with Antagonist PT2385 | |||||||||
Components |
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Keywords | transcription/transcription inhibitor / Complex / Antagonist / Transcription factor / transcription-transcription inhibitor complex | |||||||||
Function / homology | Function and homology information Cellular response to hypoxia / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / myoblast fate commitment / norepinephrine biosynthetic process / Regulation of gene expression by Hypoxia-inducible Factor / Endogenous sterols / nuclear aryl hydrocarbon receptor complex ...Cellular response to hypoxia / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / myoblast fate commitment / norepinephrine biosynthetic process / 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 dopamine biosynthetic process / positive regulation of hormone biosynthetic process / aryl hydrocarbon receptor complex / regulation of protein neddylation / positive regulation of protein sumoylation / Neddylation / norepinephrine metabolic process / surfactant homeostasis / epithelial cell maturation / embryonic placenta development / cobalt ion binding / aryl hydrocarbon receptor binding / hemopoiesis / positive regulation of vascular endothelial growth factor production / blood vessel remodeling / cis-regulatory region sequence-specific DNA binding / visual perception / regulation of heart rate / erythrocyte differentiation / lung development / mitochondrion organization / mRNA transcription by RNA polymerase II / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of inflammatory response / response to toxic substance / RNA polymerase II transcription regulator complex / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / nuclear receptor activity / sequence-specific double-stranded DNA binding / cellular response to hypoxia / positive regulation of cold-induced thermogenesis / gene expression / cellular response to oxidative stress / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / angiogenesis / sequence-specific DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / response to hypoxia / nuclear body / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Wu, D. / Su, X. / Lu, J. / Li, S. / Hood, B. / Vasile, S. / Potluri, N. / Diao, X. / Kim, Y. / Khorasanizadeh, S. / Rastinejad, F. | |||||||||
Funding support | United States, China, 2items
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Citation | Journal: Nat. Chem. Biol. / Year: 2019 Title: Bidirectional modulation of HIF-2 activity through chemical ligands. Authors: Wu, D. / Su, X. / Lu, J. / Li, S. / Hood, B.L. / Vasile, S. / Potluri, N. / Diao, X. / Kim, Y. / Khorasanizadeh, S. / Rastinejad, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e3s.cif.gz | 243.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e3s.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 6e3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e3s_validation.pdf.gz | 744.3 KB | Display | wwPDB validaton report |
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Full document | 6e3s_full_validation.pdf.gz | 755.6 KB | Display | |
Data in XML | 6e3s_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 6e3s_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/6e3s ftp://data.pdbj.org/pub/pdb/validation_reports/e3/6e3s | HTTPS FTP |
-Related structure data
Related structure data | 6e3tC 6e3uC 4zp4S 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 / Plasmid: pMKH / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53762 |
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#2: Protein | Mass: 42156.961 Da / Num. of mol.: 1 / Mutation: W318A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Epas1, Hif2a / Plasmid: PSJ2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P97481 |
#3: Chemical | ChemComp-79A / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2% TACSIMATE, PH 7.0, 6% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 14037 / % possible obs: 99 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.9→2.95 Å / Rmerge(I) obs: 0.765 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZP4 Resolution: 3→48.948 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.01
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.948 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 164.7007 Å / Origin y: -117.9064 Å / Origin z: 156.1202 Å
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Refinement TLS group | Selection details: all |