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- PDB-7lfc: Structure of importin a3 bound to p50 NLS -

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Basic information

Entry
Database: PDB / ID: 7lfc
TitleStructure of importin a3 bound to p50 NLS
Components
  • Importin subunit alpha-3
  • Nuclear factor NF-kappa-B p105 subunit
KeywordsPROTEIN TRANSPORT / NUCLEAR IMPORT / IMPORTIN ALPHA 3 / NLS / NF-kB / p50 / p65
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 / IkBA variant leads to EDA-ID / dopamine secretion / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / Regulated proteolysis of p75NTR / negative regulation of interleukin-12 production / 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 / Interleukin-1 processing / cellular response to interleukin-6 / 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 / 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 / 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 / ISG15 antiviral mechanism / 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 / Interleukin-1 signaling / HCMV Early Events / cellular response to mechanical stimulus / cellular response to nicotine / protein import into nucleus / 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 / gene expression / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / nuclear membrane / cellular response to lipopolysaccharide / 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 / 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 / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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
Importin subunit alpha-3 / Nuclear factor NF-kappa-B p105 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 16, 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

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Assembly

Deposited unit
A: Importin subunit alpha-3
B: Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)59,7322
Polymers59,7322
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-5 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.650, 59.070, 86.090
Angle α, β, γ (deg.)90.000, 96.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Importin subunit alpha-3 / / Importin alpha Q1 / Qip1 / Karyopherin subunit alpha-4


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
#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.: 105 / 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: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tbk

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
RfactorNum. reflection% reflection
Rfree0.2203 1381 5.02 %
Rwork0.1871 26155 -
obs0.1887 27536 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.68 Å2 / Biso mean: 63.3367 Å2 / Biso min: 28.53 Å2
Refinement stepCycle: final / Resolution: 2.1→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 105 3371
Biso mean---53.74 -
Num. residues----426
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 (%)
2.1-2.170.31221270.26572376250390
2.17-2.260.27471350.241526162751100
2.26-2.360.28661380.213126432781100
2.36-2.490.24421390.204326082747100
2.49-2.640.20941450.204126432788100
2.64-2.850.24591530.206325982751100
2.85-3.130.24621350.20522647278299
3.13-3.580.26531320.19926482780100
3.58-4.490.17381460.161226692815100
4.49-14.930.19871310.16722707283899
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)
13.40341.6029-0.55197.47211.94643.8758-0.0410.2139-0.0129-0.04730.0943-0.2788-0.43280.0672-0.0540.2445-0.0020.0040.3066-0.01650.290832.21190.379933.3555
24.19-0.06950.47512.69590.44313.55530.19241.1808-0.6268-0.5755-0.16380.04010.3687-0.3427-0.09870.447-0.02410.05320.6445-0.20920.4470.6041-22.362314.172
38.81233.36685.67971.42382.03714.26170.0516-0.31190.22980.0598-0.56541.71530.2647-1.3390.46290.73970.11470.06690.68480.03380.811619.9211.837529.0474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 72 through 236 )A72 - 236
2X-RAY DIFFRACTION2chain 'A' and (resid 237 through 485 )A237 - 485
3X-RAY DIFFRACTION3chain 'B' and (resid 432 through 443 )B432 - 443

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