+Open data
-Basic information
Entry | Database: PDB / ID: 7rg5 | ||||||
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Title | Importin alpha3 in complex with p50 NLS | ||||||
Components |
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Keywords | TRANSPORT PROTEIN/VIRAL PROTEIN / complex / transportin / importin / TRANSPORT PROTEIN-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information negative regulation of protein metabolic process => GO:0051248 / transcription coactivator binding => GO:0001223 / negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / regulation of transcription initiation by RNA polymerase II / positive regulation of hyaluronan biosynthetic process / neutrophil degranulation / membrane protein intracellular domain proteolysis ...negative regulation of protein metabolic process => GO:0051248 / transcription coactivator binding => GO:0001223 / negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / regulation of transcription initiation by RNA polymerase II / positive regulation of hyaluronan biosynthetic process / neutrophil degranulation / membrane protein intracellular domain proteolysis / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / dopamine secretion / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / negative regulation of interleukin-12 production / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / NS1 Mediated Effects on Host Pathways / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / cellular response to interleukin-6 / Interleukin-1 processing / cellular response to dsRNA / actinin binding / cellular response to angiotensin / interleukin-1-mediated signaling pathway / positive regulation of miRNA metabolic process / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / transcription factor binding / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / cellular response to interleukin-1 / positive regulation of type I interferon production / Purinergic signaling in leishmaniasis infection / nuclear pore / stress-activated MAPK cascade / response to muscle stretch / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / MAP3K8 (TPL2)-dependent MAPK1/3 activation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Activation of NF-kappaB in B cells / TAK1-dependent IKK and NF-kappa-B activation / ISG15 antiviral mechanism / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / FCERI mediated NF-kB activation / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / HCMV Early Events / cellular response to nicotine / cellular response to mechanical stimulus / specific granule lumen / protein import into nucleus / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / gene expression / Senescence-Associated Secretory Phenotype (SASP) / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / secretory granule lumen / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / Neutrophil degranulation / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Smith, K.M. / Tsimbalyuk, S. / 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 | 7rg5.cif.gz | 206.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rg5.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 7rg5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/7rg5 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/7rg5 | HTTPS FTP |
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-Related structure data
Related structure data | 7rfxC 7rfyC 7rfzC 7rg0C 7rg2C 7rg3C 7rg4C 7rg6C 6bvzS 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: 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: 4975.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19838-3 |
#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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium thiocyanate and 20% PEG3350 |
-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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 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: 2.15→85.72 Å / Num. obs: 26271 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 43.16 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.15→2.21 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2043 / Rpim(I) all: 0.31 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BVZ Resolution: 2.15→48.7 Å / SU ML: 0.2738 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7566 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: 60.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→48.7 Å
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Refine LS restraints |
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LS refinement shell |
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