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Yorodumi- PDB-8fub: Crystal structure of human Importin alpha 3 in complex with Hendr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fub | ||||||
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Title | Crystal structure of human Importin alpha 3 in complex with Hendra virus matrix protein NLS1 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Importin / nuclear transport | ||||||
Function / homology | Function and homology information dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / virion assembly / nuclear pore / virion component / ISG15 antiviral mechanism ...dopamine secretion / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / virion assembly / nuclear pore / virion component / ISG15 antiviral mechanism / protein import into nucleus / gene expression / nuclear membrane / host cell cytoplasm / structural constituent of virion / host cell nucleus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hendra virus horse/Australia/Hendra/1994 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Donnelly, C.M. / Basler, C.F. / Scott, C. / Forwood, J.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: Viruses / Year: 2023 Title: Henipavirus Matrix Protein Employs a Non-Classical Nuclear Localization Signal Binding Mechanism. Authors: Donnelly, C.M. / Vogel, O.A. / Edwards, M.R. / Taylor, P.E. / Roby, J.A. / Forwood, J.K. / Basler, C.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fub.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fub.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fub ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fub | HTTPS FTP |
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-Related structure data
Related structure data | 8fuaC 8fucC 6bvzS 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: 50325.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA4, QIP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O00629 |
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#2: Protein/peptide | Mass: 2136.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hendra virus horse/Australia/Hendra/1994 / References: UniProt: O89341 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1M sodium HEPES,0.72M sodium citrate, 1% dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 25, 2019 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→29.78 Å / Num. obs: 13681 / % possible obs: 99.9 % / Redundancy: 11.3 % / Biso Wilson estimate: 65.77 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.181 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.75→2.9 Å / Rmerge(I) obs: 1.032 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1966 / CC1/2: 0.887 / Rpim(I) all: 0.446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BVZ Resolution: 2.75→29.78 Å / SU ML: 0.3291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2044 / Stereochemistry target values: CDL v1.2
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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 mean: 72.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→29.78 Å
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Refine LS restraints |
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LS refinement shell |
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