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Yorodumi- PDB-8he0: Crystal structure of importin-alpha1 bound to the HIF-1alpha nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8he0 | ||||||
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Title | Crystal structure of importin-alpha1 bound to the HIF-1alpha nuclear localization signal (wild-type) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / NLS | ||||||
Function / homology | Function and homology information epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis ...epithelial cell differentiation involved in mammary gland alveolus development / neural fold elevation formation / iris morphogenesis / positive regulation of chemokine-mediated signaling pathway / hypoxia-inducible factor-1alpha signaling pathway / elastin metabolic process / glandular epithelial cell maturation / regulation of transforming growth factor beta2 production / connective tissue replacement involved in inflammatory response wound healing / cardiac ventricle morphogenesis / negative regulation of mesenchymal cell apoptotic process / hemoglobin biosynthetic process / positive regulation of hormone biosynthetic process / mesenchymal cell apoptotic process / retina vasculature development in camera-type eye / positive regulation of mitophagy / Cellular response to hypoxia / intestinal epithelial cell maturation / negative regulation of growth / regulation of protein neddylation / collagen metabolic process / PTK6 Expression / intracellular oxygen homeostasis / Sensing of DNA Double Strand Breaks / negative regulation of bone mineralization / entry of viral genome into host nucleus through nuclear pore complex via importin / B-1 B cell homeostasis / vascular endothelial growth factor production / positive regulation of viral life cycle / transcription regulator activator activity / dopaminergic neuron differentiation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / NLS-dependent protein nuclear import complex / lactate metabolic process / STAT3 nuclear events downstream of ALK signaling / postsynapse to nucleus signaling pathway / positive regulation of cytokine production involved in inflammatory response / negative regulation of thymocyte apoptotic process / positive regulation of vascular endothelial growth factor receptor signaling pathway / motile cilium / positive regulation of signaling receptor activity / insulin secretion involved in cellular response to glucose stimulus / negative regulation of TOR signaling / response to muscle activity / response to iron ion / neural crest cell migration / Regulation of gene expression by Hypoxia-inducible Factor / regulation of glycolytic process / embryonic hemopoiesis / nuclear import signal receptor activity / DNA-binding transcription repressor activity / nuclear localization sequence binding / DNA-binding transcription activator activity / PTK6 promotes HIF1A stabilization / regulation of aerobic respiration / digestive tract morphogenesis / muscle cell cellular homeostasis / NLS-bearing protein import into nucleus / positive regulation of neuroblast proliferation / axonal transport of mitochondrion / positive regulation of epithelial cell migration / bone mineralization / heart looping / outflow tract morphogenesis / E-box binding / intracellular glucose homeostasis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / TOR signaling / positive regulation of vascular endothelial growth factor production / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / embryonic placenta development / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / cellular response to interleukin-1 / cis-regulatory region sequence-specific DNA binding / chondrocyte differentiation / positive regulation of chemokine production / axon cytoplasm / positive regulation of endothelial cell proliferation / lactation / positive regulation of glycolytic process / negative regulation of miRNA transcription / positive regulation of erythrocyte differentiation / positive regulation of nitric-oxide synthase activity / response to reactive oxygen species / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / euchromatin / visual learning / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / NOTCH1 Intracellular Domain Regulates Transcription / cerebral cortex development / cellular response to virus / transcription coactivator binding / positive regulation of miRNA transcription / histone deacetylase binding / cytoplasmic stress granule / RNA polymerase II transcription regulator complex Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Matsuura, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2023 Title: Structures of importin-alpha bound to the wild-type and an internal deletion mutant of the bipartite nuclear localization signal of HIF-1 alpha. Authors: Matsuura, Y. / Miyawaki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8he0.cif.gz | 107.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8he0.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 8he0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8he0_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 8he0_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 8he0_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 8he0_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8he0 ftp://data.pdbj.org/pub/pdb/validation_reports/he/8he0 | HTTPS FTP |
-Related structure data
Related structure data | 8he3C 6iu7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46374.152 Da / Num. of mol.: 1 / Fragment: UNP residues 72-498 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293 |
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#2: Protein/peptide | Mass: 4745.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1A / Production host: Escherichia coli (E. coli) / References: UniProt: Q16665 |
#3: 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: 3.63 Å3/Da / Density % sol: 66.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: tri-sodium citrate, HEPES, DTT |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25.07 Å / Num. obs: 65167 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.998 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3807 / CC1/2: 0.705 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IU7 Resolution: 1.8→25.07 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / Phase error: 20.21 / 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 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.8247 Å
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