+Open data
-Basic information
Entry | Database: PDB / ID: 7lfc | |||||||||||||||
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Title | Structure of importin a3 bound to p50 NLS | |||||||||||||||
Components |
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Keywords | PROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA 3 / NLS / NF-kB / p50 / p65 | |||||||||||||||
Function / homology | Function and homology information 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 / 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 / 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 / cellular response to interleukin-17 / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / NF-kappaB p50/p65 complex / 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 / Regulated proteolysis of p75NTR / RIP-mediated NFkB activation via ZBP1 / NS1 Mediated Effects on Host Pathways / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / cellular response to dsRNA / cellular response to interleukin-6 / Interleukin-1 processing / actinin binding / cellular response to angiotensin / Regulation of NFE2L2 gene expression / negative regulation of protein metabolic process / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of miRNA metabolic process / 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 / nuclear pore / 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 / Activation of NF-kappaB in B cells / transcription coregulator activity / 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 / cellular response to virus / ISG15 antiviral mechanism / 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 / HCMV Early Events / Interleukin-1 signaling / cellular response to nicotine / cellular response to mechanical stimulus / specific granule lumen / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / cellular response to tumor necrosis factor / gene expression / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / nuclear membrane / secretory granule lumen / transcription regulator complex / transcription by RNA polymerase II / 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 / apoptotic process / chromatin binding / Neutrophil degranulation / chromatin / 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 / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Florio, T.J. / Lokareddy, R.K. / Cingolani, G. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lfc.cif.gz | 182.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lfc.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 7lfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lfc_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
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Full document | 7lfc_full_validation.pdf.gz | 446.7 KB | Display | |
Data in XML | 7lfc_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 7lfc_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/7lfc ftp://data.pdbj.org/pub/pdb/validation_reports/lf/7lfc | HTTPS FTP |
-Related structure data
Related structure data | 7leqC 7letC 7leuC 7lf4C 5tbkS C: citing same article (ref.) S: Starting model for refinement |
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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: 57941.387 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 (E. coli) / References: UniProt: O00629 |
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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.) Homo sapiens (human) / References: UniProt: P19838 |
#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: 2.02 Å3/Da / Density % sol: 38.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M potassium thiocyanate, 20% PEG3350, 0.1 M BIS-TRIS pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.953 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. obs: 27642 / % possible obs: 98.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.044 / Rsym value: 0.064 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2009 / CC1/2: 0.815 / Rpim(I) all: 0.412 / Rsym value: 0.552 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5tbk Resolution: 2.1→14.93 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02 / 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: 147.68 Å2 / Biso mean: 63.3367 Å2 / Biso min: 28.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→14.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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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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