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- PDB-7let: Structure of importin a2 bound to the p50- and p65-NLSs -

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Basic information

Entry
Database: PDB / ID: 7let
TitleStructure of importin a2 bound to the p50- and p65-NLSs
Components
  • Importin subunit alpha-1
  • Nuclear factor NF-kappa-B p105 subunit
  • Transcription factor p65
KeywordsPROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA / NLS / NF-kB / p50 / p65
Function / homology
Function and homology information


: / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / 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 ...: / negative regulation of vitamin D biosynthetic process / I-kappaB/NF-kappaB complex / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / 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 / toll-like receptor TLR6:TLR2 signaling pathway / IkBA variant leads to EDA-ID / Sensing of DNA Double Strand Breaks / positive regulation of Schwann cell differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / positive regulation of lipid storage / cellular response to peptidoglycan / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / ankyrin repeat binding / SUMOylation of immune response proteins / NLS-dependent protein nuclear import complex / CLEC7A/inflammasome pathway / RIP-mediated NFkB activation via ZBP1 / postsynapse to nucleus signaling pathway / negative regulation of protein sumoylation / Interleukin-1 processing / defense response to tumor cell / cellular response to interleukin-6 / nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to dsRNA / actinin binding / positive regulation of macrophage derived foam cell differentiation / response to UV-B / negative regulation of non-canonical NF-kappaB signal transduction / signal transduction involved in regulation of gene expression / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / positive regulation of leukocyte adhesion to vascular endothelial cell / Regulation of NFE2L2 gene expression / interleukin-1-mediated signaling pathway / nuclear import signal receptor activity / NF-kappaB complex / vascular endothelial growth factor signaling pathway / toll-like receptor 4 signaling pathway / positive regulation of amyloid-beta formation / cellular response to hepatocyte growth factor stimulus / response to cobalamin / phosphate ion binding / positive regulation of T cell receptor signaling pathway / cellular response to lipoteichoic acid / response to muramyl dipeptide / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / cellular response to interleukin-1 / general transcription initiation factor binding / cellular response to angiotensin / positive regulation of vascular endothelial growth factor production / positive regulation of cholesterol efflux / canonical NF-kappaB signal transduction / hair follicle development / response to amino acid / positive regulation of transcription initiation by RNA polymerase II / neuropeptide signaling pathway / NF-kappaB binding / cellular defense response / Purinergic signaling in leishmaniasis infection / RNA polymerase II core promoter sequence-specific DNA binding / response to cAMP / tumor necrosis factor-mediated signaling pathway / JNK cascade / response to muscle stretch / antiviral innate immune response / positive regulation of interleukin-12 production / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / negative regulation of insulin receptor signaling pathway / response to cytokine / response to interleukin-1 / negative regulation of miRNA transcription / NF-kB is activated and signals survival / peptide binding / protein sequestering activity / negative regulation of angiogenesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / liver development / response to progesterone / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / positive regulation of interleukin-1 beta production / response to ischemia / animal organ morphogenesis / positive regulation of interleukin-8 production / RNA polymerase II transcription regulatory region sequence-specific DNA binding / negative regulation of extrinsic apoptotic signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / response to insulin / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain ...Nuclear factor NF-kappa-B, p105 subunit / : / Transcription factor RelA (p65) / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / ig-like, plexins, transcription factors / IPT domain / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / p53-like transcription factor, DNA-binding / Death-like domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Alpha Horseshoe / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like fold / Mainly Alpha
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit / Importin subunit alpha-1 / Transcription factor p65
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsFlorio, T.J. / Lokareddy, R.K. / Cingolani, G.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122844 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA56036 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD017987 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)OD023479 United States
CitationJournal: 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
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Importin subunit alpha-1
B: Nuclear factor NF-kappa-B p105 subunit
C: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)51,0673
Polymers51,0673
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint5 kcal/mol
Surface area18720 Å2
Unit cell
Length a, b, c (Å)77.944, 91.273, 97.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 46386.055 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 (E. coli) / References: UniProt: P52293
#2: Protein/peptide Nuclear factor NF-kappa-B p105 subunit / DNA-binding factor KBF1 / EBP-1 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1


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: Protein/peptide Transcription factor p65 / Nuclear factor NF-kappa-B p65 subunit / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 3


Mass: 2890.410 Da / Num. of mol.: 1
Fragment: Nuclear localization signal motif, residues 294-315
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.6 Na Citrate, 100 mM HEPES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1y2a

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
RfactorNum. reflection% reflection
Rfree0.2415 1211 4.96 %
Rwork0.1981 23211 -
obs0.2003 24422 88.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.53 Å2 / Biso mean: 68.9605 Å2 / Biso min: 38.49 Å2
Refinement stepCycle: final / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 32 3390
Biso mean---62.54 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.50.3796900.36031606169656
2.5-2.610.37571100.33772153226375
2.61-2.750.37141330.32422506263988
2.75-2.920.36961400.28582748288895
2.92-3.140.32131510.25962838298999
3.14-3.460.27571530.22272826297998
3.46-3.950.22141430.18472873301698
3.95-4.950.20041460.15072842298897
4.95-150.17731450.14682819296492
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.6102-3.85331.93794.2526-4.25527.6032-0.0764-0.13170.42860.92490.0055-0.3588-0.5054-0.1050.14090.648-0.12440.04150.3845-0.03770.6007-3.802860.0131-16.8338
22.6212-0.5985-0.63526.0508-0.42452.81180.0615-0.12490.14940.12040.10560.0305-0.14310.0136-0.17530.3625-0.0236-0.00580.2910.02610.3185-5.466839.6795-15.0655
36.3478-3.12470.95184.8336-1.58938.18730.32440.2071-0.4152-0.5653-0.06410.24210.37010.1123-0.26310.48440.0165-0.03090.26330.00060.45881.386122.0979-13.765
44.7406-1.46062.95973.6383-0.74315.45970.1374-0.0385-0.2218-0.4155-0.04890.25650.3267-0.1016-0.10570.45140.04210.02240.33980.03130.49495.995713.5703-1.8934
53.9299-0.21540.92315.6236-0.81595.01530.0903-0.6167-0.41490.15670.06650.40520.0747-0.5031-0.11730.4314-0.00940.03010.4920.1190.53378.71385.587516.6055
63.5660.6253-0.38915.4073-0.30675.7471-0.0483-0.8664-0.09421.63310.27050.2677-0.2744-0.6726-0.29091.11910.0240.10411.1320.19080.68444.88214.208332.6917
75.29323.9252-5.51757.119-5.75926.36310.0779-0.7599-0.32420.1292-0.3128-1.83770.53151.08680.43690.51390.06-0.04110.69950.05180.63292.79440.997-8.254
87.2477-4.69013.4225.70682.47099.8728-0.2324-0.5463-1.34781.32140.24940.89821.0620.4255-0.28220.73110.05470.03610.73210.24770.8773-2.760110.92657.7594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 75 through 105 )E75 - 105
2X-RAY DIFFRACTION2chain 'E' and (resid 106 through 245 )E106 - 245
3X-RAY DIFFRACTION3chain 'E' and (resid 246 through 278 )E246 - 278
4X-RAY DIFFRACTION4chain 'E' and (resid 279 through 363 )E279 - 363
5X-RAY DIFFRACTION5chain 'E' and (resid 364 through 454 )E364 - 454
6X-RAY DIFFRACTION6chain 'E' and (resid 455 through 497 )E455 - 497
7X-RAY DIFFRACTION7chain 'B' and (resid 435 through 442 )B435 - 442
8X-RAY DIFFRACTION8chain 'C' and (resid 289 through 294 )C289 - 294

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