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- PDB-7leu: Structure of importin a2 bound to p65-NLS -

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Basic information

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


acetaldehyde metabolic process / prolactin signaling pathway / 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 Schwann cell differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / cellular response to peptidoglycan ...acetaldehyde metabolic process / prolactin signaling pathway / 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 Schwann cell differentiation / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / cellular response to peptidoglycan / Regulated proteolysis of p75NTR / ankyrin repeat binding / RIP-mediated NFkB activation via ZBP1 / SUMOylation of immune response proteins / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / negative regulation of protein sumoylation / postsynapse to nucleus signaling pathway / defense response to tumor cell / nucleotide-binding oligomerization domain containing 2 signaling pathway / Interleukin-1 processing / cellular response to interleukin-6 / actinin binding / NF-kappaB complex / negative regulation of non-canonical NF-kappaB signal transduction / cellular response to angiotensin / response to UV-B / vascular endothelial growth factor signaling pathway / interleukin-1-mediated signaling pathway / Regulation of NFE2L2 gene expression / positive regulation of leukocyte adhesion to vascular endothelial cell / nuclear import signal receptor activity / positive regulation of miRNA metabolic process / toll-like receptor 4 signaling pathway / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cellular response to hepatocyte growth factor stimulus / positive regulation of amyloid-beta formation / positive regulation of T cell receptor signaling pathway / response to cobalamin / phosphate ion binding / host cell / non-canonical NF-kappaB signal transduction / cellular response to lipoteichoic acid / TRAF6 mediated NF-kB activation / response to muramyl dipeptide / The NLRP3 inflammasome / general transcription initiation factor binding / Transcriptional Regulation by VENTX / hair follicle development / NF-kappaB binding / neuropeptide signaling pathway / positive regulation of vascular endothelial growth factor production / RNA polymerase II core promoter sequence-specific DNA binding / canonical NF-kappaB signal transduction / response to amino acid / cellular response to interleukin-1 / cellular defense response / Purinergic signaling in leishmaniasis infection / negative regulation of insulin receptor signaling pathway / response to cAMP / tumor necrosis factor-mediated signaling pathway / response to muscle stretch / positive regulation of interleukin-12 production / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / negative regulation of angiogenesis / response to interleukin-1 / negative regulation of miRNA transcription / liver development / response to progesterone / response to organic substance / positive regulation of interleukin-1 beta production / response to cytokine / response to ischemia / positive regulation of interleukin-8 production / Dectin-1 mediated noncanonical NF-kB signaling / negative regulation of extrinsic apoptotic signaling pathway / Activation of NF-kappaB in B cells / peptide binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / animal organ morphogenesis / protein catabolic process / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / transcription coactivator binding / negative regulation of protein catabolic process / chromatin DNA binding / CLEC7A (Dectin-1) signaling / PKMTs methylate histone lysines / cellular response to hydrogen peroxide / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / cytoplasmic stress granule / cytokine-mediated signaling pathway / positive regulation of interleukin-6 production / cellular response to nicotine
Similarity search - Function
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. ...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. / 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 / Armadillo-like helical / Immunoglobulin E-set / Armadillo-type fold / Immunoglobulin-like fold
Similarity search - Domain/homology
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: 2.82 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: Transcription factor p65
C: Transcription factor p65


Theoretical massNumber of molelcules
Total (without water)52,1673
Polymers52,1673
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint5 kcal/mol
Surface area18800 Å2
Unit cell
Length a, b, c (Å)78.556, 90.857, 99.879
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 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.: 2
Fragment: Nuclear localization signal motif, residues 294-315
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04206
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.55M Na citrate, 100mM HEPES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.81→15 Å / Num. obs: 17271 / % possible obs: 97.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 70.1 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.073 / Rsym value: 0.111 / Net I/σ(I): 14.5
Reflection shellResolution: 2.81→2.91 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1551 / CC1/2: 0.718 / Rpim(I) all: 0.73 / Rsym value: 0.53 / % possible all: 89.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1y2a

1y2a


Resolution: 2.82→15 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 857 5 %
Rwork0.2007 16277 -
obs0.2025 17134 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 161.25 Å2 / Biso mean: 80.126 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.82→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 1 3347
Biso mean---67.36 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.82-2.990.35471250.34722412253787
2.99-3.220.33651430.33052709285298
3.22-3.540.34731450.27772730287598
3.54-4.050.23041460.19762762290899
4.05-5.060.22491460.16362795294199
5.06-150.1681520.14962869302198
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)
12.1335-0.1331-0.49073.4876-0.80780.78060.0663-0.08710.03930.12040.0987-0.0267-0.20640.1137-0.00350.7236-0.02020.00170.7230.00240.5772-5.228342.9905-15.9683
21.5141-0.66551.15461.5656-1.48333.30270.0438-0.4327-0.25850.09370.1360.29520.0745-0.3661-0.01320.6941-0.03030.03230.81580.04810.83266.439510.45819.7185
30.9019-0.49170.50250.66230.21970.90.0018-0.43960.1936-0.1991-0.2516-0.5972-0.12880.77760.03391.14930.0032-0.07851.05110.0380.9963.447741.2023-9.5921
40.9329-0.28850.20160.45710.27840.6360.03960.0072-0.36670.63280.0956-0.22080.17650.0745-0.00621.0410.0227-0.04851.15790.18651.0915-2.733711.12988.3481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 75 through 245 )E75 - 245
2X-RAY DIFFRACTION2chain 'E' and (resid 246 through 497 )E246 - 497
3X-RAY DIFFRACTION3chain 'B' and (resid 435 through 442 )B435 - 442
4X-RAY DIFFRACTION4chain 'C' and (resid 289 through 294 )C289 - 294

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