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Open data
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Basic information
Entry | Database: PDB / ID: 7let | |||||||||||||||
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Title | Structure of importin a2 bound to the p50- and p65-NLSs | |||||||||||||||
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![]() | PROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA / NLS / NF-kB / p50 / p65 | |||||||||||||||
Function / homology | ![]() negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / acetaldehyde metabolic process / prolactin signaling pathway / cellular response to interleukin-17 ...negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / positive regulation of hyaluronan biosynthetic process / antibacterial innate immune response / mammary gland involution / acetaldehyde metabolic process / prolactin signaling pathway / 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 / positive regulation of Schwann 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 / cellular response to peptidoglycan / negative regulation of interleukin-12 production / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / Regulated proteolysis of p75NTR / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / negative regulation of protein sumoylation / defense response to tumor cell / postsynapse to nucleus signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to interleukin-6 / Interleukin-1 processing / cellular response to dsRNA / negative regulation of non-canonical NF-kappaB signal transduction / actinin binding / cellular response to angiotensin / response to UV-B / NF-kappaB complex / negative regulation of protein metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / vascular endothelial growth factor signaling pathway / positive regulation of miRNA metabolic process / non-canonical NF-kappaB signal transduction / nuclear import signal receptor activity / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / NLS-bearing protein import into nucleus / response to cobalamin / positive regulation of T cell receptor signaling pathway / phosphate ion binding / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / general transcription initiation factor binding / neuropeptide signaling pathway / Transcriptional Regulation by VENTX / NF-kappaB binding / hair follicle development / cellular response to interleukin-1 / positive regulation of vascular endothelial growth factor production / positive regulation of transcription initiation by RNA polymerase II / response to amino acid / RNA polymerase II core promoter sequence-specific DNA binding / cellular defense response / Purinergic signaling in leishmaniasis infection / canonical NF-kappaB signal transduction / antiviral innate immune response / JNK cascade / negative regulation of insulin receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / response to cAMP / response to muscle stretch / positive regulation of interleukin-12 production / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / response to interleukin-1 / negative regulation of angiogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / negative regulation of miRNA transcription / liver development / positive regulation of interleukin-1 beta production / response to cytokine / positive regulation of interleukin-8 production / response to ischemia / response to progesterone / negative regulation of extrinsic apoptotic signaling pathway / Dectin-1 mediated noncanonical NF-kB signaling / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / Activation of NF-kappaB in B cells / B cell receptor signaling pathway / transcription coregulator activity / peptide binding / TAK1-dependent IKK and NF-kappa-B activation Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||||||||
![]() | Florio, T.J. / Lokareddy, R.K. / Cingolani, G. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Differential recognition of canonical NF-kappa B dimers by Importin alpha 3. Authors: Florio, T.J. / Lokareddy, R.K. / Yeggoni, D.P. / Sankhala, R.S. / Ott, C.A. / Gillilan, R.E. / Cingolani, G. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.8 KB | Display | ![]() |
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PDB format | ![]() | 145.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7leqC ![]() 7leuC ![]() 7lf4C ![]() 7lfcC ![]() 1y2aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46386.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1790.114 Da / Num. of mol.: 1 Fragment: Nuclear localization signal motif, residues 355-368 Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Protein/peptide | Mass: 2890.410 Da / Num. of mol.: 1 Fragment: Nuclear localization signal motif, residues 294-315 Source method: obtained synthetically / Source: (synth.) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.6 Na Citrate, 100 mM HEPES pH 6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 24702 / % possible obs: 89.2 % / Redundancy: 3.1 % / Biso Wilson estimate: 51.6 Å2 / CC1/2: 0.988 / Rpim(I) all: 0.08 / Rsym value: 0.124 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.2 % / Num. unique obs: 1570 / CC1/2: 0.409 / Rpim(I) all: 0.708 / Rsym value: 0.816 / % possible all: 57.8 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1y2a Resolution: 2.4→15 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.69 / Stereochemistry target values: ML
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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 max: 154.53 Å2 / Biso mean: 68.9605 Å2 / Biso min: 38.49 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→15 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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