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Yorodumi- PDB-6bvv: Nipah virus W protein C-terminus in complex with Importin alpha 3 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bvv | ||||||
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Title | Nipah virus W protein C-terminus in complex with Importin alpha 3 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Complex / Nipah virus / Importin / Karyopherin / phosphoprotein / W | ||||||
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 / nuclear pore / ISG15 antiviral mechanism / protein import into nucleus / gene expression ...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 / nuclear pore / ISG15 antiviral mechanism / protein import into nucleus / gene expression / nuclear membrane / amyloid fibril formation / virus-mediated perturbation of host defense response / host cell nucleus / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Nipah virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Smith, K.M. / Tsimbalyuk, S. / Edwards, M.R. / Aragao, D. / Cross, E.M. / Basler, C.F. / Forwood, J.K. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: Structural basis for importin alpha 3 specificity of W proteins in Hendra and Nipah viruses. Authors: Smith, K.M. / Tsimbalyuk, S. / Edwards, M.R. / Cross, E.M. / Batra, J. / Soares da Costa, T.P. / Aragao, D. / Basler, C.F. / Forwood, J.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bvv.cif.gz | 102.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bvv.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/6bvv ftp://data.pdbj.org/pub/pdb/validation_reports/bv/6bvv | HTTPS FTP |
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-Related structure data
Related structure data | 6bvtC 6bvzC 6bw0C 6bw1C 6bw9C 6bwaC 6bwbC 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: 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) / Strain (production host): BL21(DE3) / References: UniProt: O00629 |
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#2: Protein/peptide | Mass: 4773.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nipah virus / Gene: P/V/C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0C1C7 |
#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: 2.07 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithium nitrate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→38.211 Å / Num. obs: 19881 / % possible obs: 98.9 % / Redundancy: 2.3 % / Rpim(I) all: 0.087 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1953 / Rpim(I) all: 0.274 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Resolution: 2.3→38.211 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.64
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→38.211 Å
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Refine LS restraints |
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LS refinement shell |
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