+Open data
-Basic information
Entry | Database: PDB / ID: 6d0b | ||||||
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Title | Crystal structure of PT1614 bound to HIF2a-B*:ARNT-B* complex | ||||||
Components |
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Keywords | TRANSCRIPTION / Hif2a / Pas B domain / ARNT / hypoxia inducible factor / EPAS1 | ||||||
Function / homology | Function and homology information 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 / visual perception / NPAS4 regulates expression of target genes / Pexophagy / positive regulation of glycolytic process / regulation of heart rate / 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 / multicellular organismal-level iron ion homeostasis / transcription coactivator binding / 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 / transcription regulator complex / sequence-specific DNA binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Du, X. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of PT1614 bound to HIF2a-B*:ARNT-B* complex Authors: Du, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6d0b.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d0b.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 6d0b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6d0b_validation.pdf.gz | 763 KB | Display | wwPDB validaton report |
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Full document | 6d0b_full_validation.pdf.gz | 770.3 KB | Display | |
Data in XML | 6d0b_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6d0b_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/6d0b ftp://data.pdbj.org/pub/pdb/validation_reports/d0/6d0b | HTTPS FTP |
-Related structure data
Related structure data | 4xt2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13538.300 Da / Num. of mol.: 1 / Fragment: residues 239-350 / Mutation: R14E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EPAS1, BHLHE73, HIF2A, MOP2, PASD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99814 |
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#2: Protein | Mass: 14243.098 Da / Num. of mol.: 1 / Fragment: residues 356-470 / Mutation: E13R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARNT, BHLHE2 / Production host: Escherichia coli (E. coli) / References: UniProt: P27540 |
#3: Chemical | ChemComp-FOV / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: Bis-Tris pH5.4, 16% PEG3350. Seeding right after setup using crushed crystals |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen vapor |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 31534 / % possible obs: 99.6 % / Redundancy: 3.6 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Χ2: 1.413 / Net I/σ(I): 27 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3121 / CC1/2: 0.608 / Rpim(I) all: 0.48 / Rrim(I) all: 0.889 / Χ2: 1.4 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XT2 Resolution: 1.6→26.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.959 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.33 Å2 / Biso mean: 23.372 Å2 / Biso min: 10.51 Å2
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Refinement step | Cycle: final / Resolution: 1.6→26.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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