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- PDB-7leq: Structure of importin a2 bound to p50 NLS -

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Basic information

Entry
Database: PDB / ID: 7leq
TitleStructure of importin a2 bound to p50 NLS
Components
  • Importin subunit alpha-1
  • Nuclear factor NF-kappa-B p105 subunit
KeywordsPROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA / NLS / NF-kB / p50
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
: / Nuclear factor NF-kappa-B, p105 subunit / 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 ...: / Nuclear factor NF-kappa-B, p105 subunit / 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 / 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 / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like fold
Similarity search - Domain/homology
Nuclear factor NF-kappa-B p105 subunit / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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 14, 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


Theoretical massNumber of molelcules
Total (without water)48,1762
Polymers48,1762
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint0 kcal/mol
Surface area18630 Å2
Unit cell
Length a, b, c (Å)78.187, 90.730, 97.465
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.6M sodium citrate, 100 Hepes pH 6.0

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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 PILATUS3 S 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→15 Å / Num. obs: 27626 / % possible obs: 81.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.091 / Net I/σ(I): 14.4
Reflection shellResolution: 2.24→2.33 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2882 / Rsym value: 0.852 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y2A

1y2a


Resolution: 2.24→14.89 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.219 1372 4.98 %
Rwork0.189 26192 -
obs0.191 27564 81.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.16 Å2 / Biso mean: 52.53 Å2 / Biso min: 22 Å2
Refinement stepCycle: final / Resolution: 2.24→14.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3276 0 0 146 3422
Biso mean---52.45 -
Num. residues----430
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.320.25811340.25492729286387
2.32-2.420.27091410.23912747288887
2.42-2.530.27371370.22872659279684
2.53-2.660.27151430.2252629277283
2.66-2.820.25371470.20682712285986
2.82-3.040.22751380.21062682282084
3.04-3.340.23451360.21272601273781
3.34-3.820.23461360.1842628276482
3.82-4.790.2011300.15212428255874
4.79-14.890.15891300.15942377250771
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)
12.3422-0.32810.17243.1179-0.82494.78230.1807-0.06560.24950.23570.1297-0.1004-0.4466-0.1201-0.20780.3766-0.05480.02690.37210.00760.2949-4.392660.0831-17.1809
21.96610.4769-0.35645.2589-0.84881.83470.0114-0.00980.15450.16440.0750.0687-0.17780.0316-0.0990.2368-0.00110.01560.26950.01080.2307-7.021544.4504-14.3207
32.0279-0.6267-0.5192.87410.26781.56810.04750.0132-0.1724-0.0786-0.0035-0.06290.1180.0157-0.01310.29270.0051-0.00450.23280.01440.3047-1.942828.5698-16.9127
41.3799-1.33440.3024.0071-0.71052.89330.17820.0242-0.1978-0.1456-0.10140.25090.21630.0845-0.06530.27640.009-0.01630.26740.01660.29282.672818.4472-9.3722
53.0948-0.39811.27532.8442-0.82662.89750.0122-0.5134-0.16970.12990.05710.27230.0209-0.4475-0.0610.26680.02290.02450.35150.07860.35678.86877.813512.226
63.05590.32710.34465.15310.13860.7640.1613-1.1792-0.10931.7049-0.14220.3728-0.1665-0.8185-0.03071.0256-0.01450.10991.33760.18860.55585.26053.578632.4928
78.8652-0.9966-0.3195.10731.12435.2015-0.49890.19260.33680.26320.5732-0.41430.21850.1418-0.07130.4306-0.1121-0.03980.5188-0.01370.25122.509441.9708-8.7209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'E' AND (RESID 75 THROUGH 104 )E0
2X-RAY DIFFRACTION2CHAIN 'E' AND (RESID 105 THROUGH 202 )E0
3X-RAY DIFFRACTION3CHAIN 'E' AND (RESID 203 THROUGH 245 )E0
4X-RAY DIFFRACTION4CHAIN 'E' AND (RESID 246 THROUGH 322 )E0
5X-RAY DIFFRACTION5CHAIN 'E' AND (RESID 323 THROUGH 452 )E0
6X-RAY DIFFRACTION6CHAIN 'E' AND (RESID 453 THROUGH 497 )E0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 436 THROUGH 442 )B0

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