+Open data
-Basic information
Entry | Database: PDB / ID: 7rg4 | ||||||
---|---|---|---|---|---|---|---|
Title | Importin alpha2 in complex with p50 NLS | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN/VIRAL PROTEIN / complex / transportin / importin / TRANSPORT PROTEIN-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex ...negative regulation of calcidiol 1-monooxygenase activity / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / Sensing of DNA Double Strand Breaks / IkBA variant leads to EDA-ID / positive regulation of macrophage derived foam cell differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of lipid storage / positive regulation of viral life cycle / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / RIP-mediated NFkB activation via ZBP1 / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / cellular response to dsRNA / postsynapse to nucleus signaling pathway / Interleukin-1 processing / cellular response to interleukin-6 / host cell / actinin binding / cellular response to angiotensin / Regulation of NFE2L2 gene expression / negative regulation of protein metabolic process / nuclear import signal receptor activity / positive regulation of miRNA metabolic process / nuclear localization sequence binding / NLS-bearing protein import into nucleus / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / positive regulation of transcription initiation by RNA polymerase II / canonical NF-kappaB signal transduction / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / response to cytokine / transcription coregulator activity / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / B cell receptor signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / cellular response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / negative regulation of inflammatory response / Transcriptional regulation of white adipocyte differentiation / cytoplasmic stress granule / Interleukin-1 signaling / HCMV Early Events / cellular response to mechanical stimulus / cellular response to nicotine / protein import into nucleus / histone deacetylase binding / specific granule lumen / positive regulation of canonical Wnt signaling pathway / SARS-CoV-1 activates/modulates innate immune responses / Downstream TCR signaling / cellular response to tumor necrosis factor / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / nuclear membrane / DNA-binding transcription factor binding / cellular response to lipopolysaccharide / transcription regulator complex / transcription by RNA polymerase II / postsynaptic density / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / glutamatergic synapse / apoptotic process / chromatin binding / chromatin / Neutrophil degranulation / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Smith, K.M. / Tsimbalyuk, S. / Aragao, D. / Forwood, J.K. | ||||||
Funding support | Australia, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7rg4.cif.gz | 209.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7rg4.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 7rg4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/7rg4 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/7rg4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7rfxC 7rfyC 7rfzC 7rg0C 7rg2C 7rg3C 7rg5C 7rg6C 6bvtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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 |
---|---|
#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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.45 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 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: 2.6→29.92 Å / Num. obs: 21620 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 55.95 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Rmerge(I) obs: 1.321 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2587 / Rpim(I) all: 0.63 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BVT Resolution: 2.6→29.92 Å / SU ML: 0.4112 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5483 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→29.92 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|