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Yorodumi- PDB-8he3: Crystal structure of importin-alpha1 bound to the HIF-1alpha nucl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8he3 | ||||||
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Title | Crystal structure of importin-alpha1 bound to the HIF-1alpha nuclear localization signal (delta 724-751) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / NLS | ||||||
Function / homology | Function and homology information Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus ...Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 8he3.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8he3.ent.gz | 77.4 KB | Display | PDB format |
PDBx/mmJSON format | 8he3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/8he3 ftp://data.pdbj.org/pub/pdb/validation_reports/he/8he3 | HTTPS FTP |
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-Related structure data
Related structure data | 8he0C 6iu7S C: citing same article (ref.) S: Starting model for refinement |
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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: 1881.276 Da / Num. of mol.: 1 / Mutation: deletion mutation 724-751 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HIF1A / Production host: Escherichia coli (E. coli) | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.67 Å3/Da / Density % sol: 66.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: ammonium sulfate, 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: Feb 29, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.24 Å / Num. obs: 56412 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.998 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3558 / CC1/2: 0.567 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IU7 Resolution: 1.9→38.235 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / 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: 1.9→38.235 Å
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Refine LS restraints |
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LS refinement shell |
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