+Open data
-Basic information
Entry | Database: PDB / ID: 7rfx | ||||||
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Title | Importin alpha2 in complex with MERS ORF4B | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/Viral Protein / Complex / Transportin / Importin / Virus / TRANSPORT PROTEIN / TRANSPORT PROTEIN-Viral Protein complex | ||||||
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 / host cell / cytoplasmic stress granule ...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 / host cell / cytoplasmic stress granule / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Middle East respiratory syndrome-related coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Munasinghe, T.S. / Tsimbalyuk, S. / Roby, J.A. / Aragao, D. / Forwood, J.K. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: MERS-CoV ORF4b employs an unusual binding mechanism to target IMP alpha and block innate immunity. Authors: Munasinghe, T.S. / Edwards, M.R. / Tsimbalyuk, S. / Vogel, O.A. / Smith, K.M. / Stewart, M. / Foster, J.K. / Bosence, L.A. / Aragao, D. / Roby, J.A. / 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 | 7rfx.cif.gz | 220.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rfx.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 7rfx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rf/7rfx ftp://data.pdbj.org/pub/pdb/validation_reports/rf/7rfx | HTTPS FTP |
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-Related structure data
Related structure data | 7rfyC 7rfzC 7rg0C 7rg2C 7rg3C 7rg4C 7rg5C 7rg6C 6bvtS 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: 55268.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293 |
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#2: Protein/peptide | Mass: 2711.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T2BB21 |
#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: 3.05 Å3/Da / Density % sol: 59.64 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.7M sodium citrate (pH 7.0) and 10 mM DTT |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26.93 Å / Num. obs: 42012 / % possible obs: 99.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 35.87 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 3409 / CC1/2: 0.562 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BVT Resolution: 2.1→26.93 Å / SU ML: 0.2232 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7904 Stereochemistry target values: GeoStd + Monomer Library + 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: 49.12 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→26.93 Å
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Refine LS restraints |
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LS refinement shell |
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