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- PDB-4zqd: Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zqd | ||||||
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Title | Crystal Structure of the Heterodimeric HIF-2a:ARNT Complex with the Benzoxadiazole Antagonist 0X3 | ||||||
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![]() | PROTEIN TRANSPORT/TRANSCRIPTION / ARNT / HIF-2a / 0X3 / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION complex | ||||||
Function / homology | ![]() 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 / cobalt ion binding / aryl hydrocarbon receptor binding / hemopoiesis / positive regulation of vascular endothelial growth factor production / embryonic placenta development / blood vessel remodeling / cis-regulatory region sequence-specific DNA binding / visual perception / regulation of heart rate / mitochondrion organization / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / response to toxic substance / transcription coactivator binding / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / positive regulation of cold-induced thermogenesis / gene expression / cellular response to oxidative stress / cellular response to hypoxia / DNA-binding transcription activator activity, RNA polymerase II-specific / angiogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / response to oxidative stress / sequence-specific DNA binding / transcription regulator complex / transcription by RNA polymerase II / cell differentiation / nuclear body / 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 / protein-containing complex binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F. | ||||||
![]() | ![]() Title: Structural integration in hypoxia-inducible factors. Authors: Wu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 453.2 KB | Display | ![]() |
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PDB format | ![]() | 373.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817 KB | Display | ![]() |
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Full document | ![]() | 861.4 KB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 58.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zp4SC ![]() 4zphC ![]() 4zpkC ![]() 4zprC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
#1: Protein | Mass: 43437.391 Da / Num. of mol.: 2 / Fragment: UNP residues 82-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 41200.953 Da / Num. of mol.: 2 / Fragment: UNP residues 3-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-0X3 / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.8 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: -h,-k,l / Fraction: 0.47 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.87→50 Å / Num. obs: 30404 / % possible obs: 97.9 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.089 / Rrim(I) all: 0.151 / Χ2: 1.459 / Net I/av σ(I): 8.924 / Net I/σ(I): 10.3 / Num. measured all: 77269 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZP4 Resolution: 2.87→48.992 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.04 / Stereochemistry target values: TWIN_LSQ_F
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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: 249.47 Å2 / Biso mean: 90.4041 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.87→48.992 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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