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Yorodumi- PDB-4zpr: Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zpr | ||||||
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Title | Crystal Structure of the Heterodimeric HIF-1a:ARNT Complex with HRE DNA | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/TRANSCRIPTION/DNA / ARNT / HIF-1a / HRE / bHLH-PAS / PROTEIN TRANSPORT-TRANSCRIPTION-DNA complex | ||||||
Function / homology | Function and homology information : / PTK6 promotes HIF1A stabilization / : / : / nuclear receptor binding => GO:0016922 / Cellular response to hypoxia / regulation of thymocyte apoptotic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling ...: / PTK6 promotes HIF1A stabilization / : / : / nuclear receptor binding => GO:0016922 / Cellular response to hypoxia / regulation of thymocyte apoptotic process / Phase I - Functionalization of compounds / Xenobiotics / Aryl hydrocarbon receptor signalling / NPAS4 regulates expression of target genes / epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / hypoxia-inducible factor-1alpha signaling pathway / Regulation of gene expression by Hypoxia-inducible Factor / elastin metabolic process / Endogenous sterols / nuclear aryl hydrocarbon receptor complex / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / digestive tract morphogenesis / positive regulation of autophagy of mitochondrion / positive regulation of hormone biosynthetic process / retina vasculature development in camera-type eye / intestinal epithelial cell maturation / aryl hydrocarbon receptor complex / negative regulation of growth / collagen metabolic process / chromatin => GO:0000785 / negative regulation of bone mineralization / intracellular oxygen homeostasis / regulation of catalytic activity / B-1 B cell homeostasis / positive regulation of protein sumoylation / vascular endothelial growth factor production / camera-type eye morphogenesis / Neddylation / Ub-specific processing proteases / E-box binding / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / dopaminergic neuron differentiation / lactate metabolic process / vasculature development / negative regulation of ossification / negative regulation of thymocyte apoptotic process / motile cilium / positive regulation of vascular endothelial growth factor receptor signaling pathway / negative regulation of TOR signaling / cartilage development / response to iron ion / response to muscle activity / blood vessel morphogenesis / neural crest cell migration / regulation of glycolytic process / embryonic hemopoiesis / embryonic placenta development / negative regulation of vasoconstriction / regulation of aerobic respiration / histone acetyltransferase binding / muscle cell cellular homeostasis / positive regulation of neuroblast proliferation / positive regulation of epithelial cell migration / axonal transport of mitochondrion / blood vessel development / heart looping / outflow tract morphogenesis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / transcription factor binding / aryl hydrocarbon receptor binding / positive regulation of macroautophagy / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / cis-regulatory region sequence-specific DNA binding / positive regulation of autophagy / response to fungicide / positive regulation of gluconeogenesis / axon cytoplasm / lactation / positive regulation of smooth muscle cell proliferation / positive regulation of erythrocyte differentiation / positive regulation of miRNA transcription / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of inflammatory response / Hsp90 protein binding / visual learning / p53 binding / response to toxic substance / RNA polymerase II transcription regulator complex / cerebral cortex development / nuclear receptor activity / histone deacetylase binding / positive regulation of angiogenesis Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.902 Å | ||||||
Authors | Wu, D. / Potluri, N. / Lu, J. / Kim, Y. / Rastinejad, F. | ||||||
Citation | Journal: Nature / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zpr.cif.gz | 146.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zpr.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 4zpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zpr_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 4zpr_full_validation.pdf.gz | 472.3 KB | Display | |
Data in XML | 4zpr_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4zpr_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/4zpr ftp://data.pdbj.org/pub/pdb/validation_reports/zp/4zpr | HTTPS FTP |
-Related structure data
Related structure data | 4zp4SC 4zphC 4zpkC 4zqdC 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 / Fragment: UNP residues 82-464 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arnt / Plasmid: pMKH / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P53762 |
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#2: Protein | Mass: 39901.574 Da / Num. of mol.: 1 / Fragment: UNP residues 13-357 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hif1a / Plasmid: pSJ2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q61221 |
#3: DNA chain | Mass: 6527.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA sense strand / Source: (synth.) Mus musculus (house mouse) |
#4: DNA chain | Mass: 6363.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: HRE DNA antisense strand / Source: (synth.) Mus musculus (house mouse) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.37 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM MES, pH 6.0, 100 mM calcium acetate, 15% PEG400 |
-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: Aug 26, 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 | Resolution: 3.9→50 Å / Num. obs: 9620 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 204.78 Å2 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Χ2: 1.115 / Net I/av σ(I): 24.722 / Net I/σ(I): 11.2 / Num. measured all: 36593 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4ZP4 Resolution: 3.902→29.845 Å / SU ML: 0.84 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 43.57 / 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: 252.28 Å2 / Biso mean: 194.6663 Å2 / Biso min: 175.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.902→29.845 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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