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- PDB-3f1p: Crystal structure of a high affinity heterodimer of HIF2 alpha an... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f1p | ||||||
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Title | Crystal structure of a high affinity heterodimer of HIF2 alpha and ARNT C-terminal PAS domains | ||||||
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![]() | TRANSCRIPTION / PAS domain / heterodimer / internal cavity / Activator / Angiogenesis / Congenital erythrocytosis / Developmental protein / Differentiation / Disease mutation / DNA-binding / Hydroxylation / Nucleus / Phosphoprotein / Transcription regulation / Ubl conjugation / Alternative splicing / Polymorphism | ||||||
Function / homology | ![]() myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation ...myoblast fate commitment / nuclear aryl hydrocarbon receptor complex / Aryl hydrocarbon receptor signalling / positive regulation of hormone biosynthetic process / Cellular response to hypoxia / aryl hydrocarbon receptor complex / regulation of protein neddylation / Transcriptional regulation of pluripotent stem cells / PTK6 Expression / positive regulation of protein sumoylation / norepinephrine metabolic process / Xenobiotics / surfactant homeostasis / Phase I - Functionalization of compounds / positive regulation of vascular endothelial growth factor receptor signaling pathway / epithelial cell maturation / Regulation of gene expression by Hypoxia-inducible Factor / aryl hydrocarbon receptor binding / positive regulation of vascular endothelial growth factor production / embryonic placenta development / blood vessel remodeling / Endogenous sterols / cis-regulatory region sequence-specific DNA binding / positive regulation of endothelial cell proliferation / NPAS4 regulates expression of target genes / Pexophagy / visual perception / regulation of heart rate / positive regulation of glycolytic process / mitochondrion organization / erythrocyte differentiation / positive regulation of erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / lung development / mRNA transcription by RNA polymerase II / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / PPARA activates gene expression / 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 / Neddylation / positive regulation of cold-induced thermogenesis / 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 / 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 / chromatin / regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Scheuermann, T.H. / Tomchick, D.R. / Machius, M. / Guo, Y. / Bruick, R.K. / Gardner, K.H. | ||||||
![]() | ![]() Title: Artificial ligand binding within the HIF2alpha PAS-B domain of the HIF2 transcription factor. Authors: Scheuermann, T.H. / Tomchick, D.R. / Machius, M. / Guo, Y. / Bruick, R.K. / Gardner, K.H. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.8 KB | Display | ![]() |
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PDB format | ![]() | 130.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 447.1 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f1nC ![]() 3f1oC ![]() 2b02S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13538.300 Da / Num. of mol.: 1 / Fragment: HIF2 alpha C-terminal PAS domain / Mutation: R247E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 14243.098 Da / Num. of mol.: 1 / Fragment: ARNT C-terminal PAS domain / Mutation: E362R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion combined with microseeding / pH: 6.5 Details: 30% PEG3350, 0.1M BisTris, 0.05M Tris, 0.017M NaCl, 0.005M DTT, pH 6.5, vapor diffusion combined with microseeding, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2007 |
Radiation | Monochromator: Custom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→26.93 Å / Num. obs: 76140 / % possible obs: 95.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 11.46 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 31.2 |
Reflection shell | Resolution: 1.17→1.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1679 / % possible all: 64.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2B02 Resolution: 1.17→26.926 Å / SU ML: 0.12 / Isotropic thermal model: individual anisotropic B values / Cross valid method: THROUGHOUT / σ(F): 1.33 / 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 / Bsol: 64.809 Å2 / ksol: 0.429 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.17→26.926 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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