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- PDB-7rg4: Importin alpha2 in complex with p50 NLS -

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Basic information

Entry
Database: PDB / ID: 7rg4
TitleImportin alpha2 in complex with p50 NLS
Components
  • Importin subunit alpha-1
  • Isoform 3 of Nuclear factor NF-kappa-B p105 subunit
KeywordsTRANSPORT PROTEIN/VIRAL PROTEIN / complex / transportin / importin / TRANSPORT PROTEIN-VIRAL PROTEIN complex
Function / homology
Function and homology information


I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / 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 / Sensing of DNA Double Strand Breaks ...I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / positive regulation of hyaluronan biosynthetic process / mammary gland involution / antibacterial innate immune response / 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 / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / CLEC7A/inflammasome pathway / NLS-dependent protein nuclear import complex / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / postsynapse to nucleus signaling pathway / cellular response to interleukin-6 / positive regulation of macrophage derived foam cell differentiation / cellular response to dsRNA / actinin binding / non-canonical NF-kappaB signal transduction / positive regulation of miRNA metabolic process / Regulation of NFE2L2 gene expression / signal transduction involved in regulation of gene expression / nuclear import signal receptor activity / TRAF6 mediated NF-kB activation / Transcriptional Regulation by VENTX / cellular response to angiotensin / The NLRP3 inflammasome / canonical NF-kappaB signal transduction / positive regulation of cholesterol efflux / positive regulation of transcription initiation by RNA polymerase II / Purinergic signaling in leishmaniasis infection / JNK cascade / response to muscle stretch / negative regulation of cytokine production involved in inflammatory response / CD209 (DC-SIGN) signaling / NF-kB is activated and signals survival / protein sequestering activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / tumor necrosis factor-mediated signaling pathway / B cell receptor signaling pathway / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Activation of NF-kappaB in B cells / cellular response to mechanical stimulus / TAK1-dependent IKK and NF-kappa-B activation / cellular response to virus / Transcriptional regulation of white adipocyte differentiation / cellular response to nicotine / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / FCERI mediated NF-kB activation / specific granule lumen / Interleukin-1 signaling / cytoplasmic stress granule / protein import into nucleus / HCMV Early Events / SARS-CoV-1 activates/modulates innate immune responses / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / host cell / cellular response to lipopolysaccharide / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / secretory granule lumen / transcription regulator complex / DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / postsynaptic density / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / inflammatory response / negative regulation of gene expression / apoptotic process / Neutrophil degranulation / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / glutamatergic synapse / 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
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: 2.6 Å
AuthorsSmith, K.M. / Tsimbalyuk, S. / Aragao, D. / Forwood, J.K.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2003636 Australia
CitationJournal: Nat Commun / Year: 2022
Title: MERS-CoV ORF4b employs an unusual binding mechanism to target IMP alpha and block innate immunity.
Authors: Munasinghe, T.S. / Edwards, M.R. / Tsimbalyuk, S. / Vogel, O.A. / Smith, K.M. / Stewart, M. / Foster, J.K. / Bosence, L.A. / Aragao, D. / Roby, J.A. / Basler, C.F. / Forwood, J.K.
History
DepositionJul 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: 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 25, 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
E: Importin subunit alpha-1
B: Isoform 3 of Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)60,2442
Polymers60,2442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-1 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.015, 89.748, 97.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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: 55268.473 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 BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide Isoform 3 of 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: 4975.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19838

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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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→29.92 Å / Num. obs: 21620 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 55.95 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 1.321 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2587 / Rpim(I) all: 0.63

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Processing

Software
NameVersionClassification
Coot1.19rc4_4035model building
PHENIX1.19rc4_4035refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BVT

6bvt


Resolution: 2.6→29.92 Å / SU ML: 0.4112 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5483
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1179 5.47 %
Rwork0.2165 20375 -
obs0.218 21554 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.67 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 0 0 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193375
X-RAY DIFFRACTIONf_angle_d0.47334592
X-RAY DIFFRACTIONf_chiral_restr0.0353553
X-RAY DIFFRACTIONf_plane_restr0.0031587
X-RAY DIFFRACTIONf_dihedral_angle_d12.16271242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.720.45551380.39652496X-RAY DIFFRACTION99.92
2.72-2.860.37941400.3162509X-RAY DIFFRACTION99.81
2.86-3.040.33531180.27212529X-RAY DIFFRACTION99.89
3.04-3.270.2651390.25922533X-RAY DIFFRACTION99.85
3.28-3.60.25521440.22722533X-RAY DIFFRACTION99.96
3.6-4.120.20571710.1872525X-RAY DIFFRACTION99.93
4.12-5.190.19251600.18032573X-RAY DIFFRACTION100
5.19-29.920.22641690.18482677X-RAY DIFFRACTION99.93

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