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- PDB-7rg5: Importin alpha3 in complex with p50 NLS -

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Basic information

Entry
Database: PDB / ID: 7rg5
TitleImportin alpha3 in complex with p50 NLS
Components
  • Importin subunit alpha-3
  • 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


negative regulation of protein metabolic process => GO:0051248 / transcription coactivator binding => GO:0001223 / negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / regulation of transcription initiation by RNA polymerase II / positive regulation of hyaluronan biosynthetic process / neutrophil degranulation / membrane protein intracellular domain proteolysis ...negative regulation of protein metabolic process => GO:0051248 / transcription coactivator binding => GO:0001223 / negative regulation of calcidiol 1-monooxygenase activity / I-kappaB/NF-kappaB complex / negative regulation of vitamin D biosynthetic process / negative regulation of cholesterol transport / regulation of transcription initiation by RNA polymerase II / positive regulation of hyaluronan biosynthetic process / neutrophil degranulation / membrane protein intracellular domain proteolysis / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / dopamine secretion / positive regulation of macrophage derived foam cell differentiation / positive regulation of lipid storage / negative regulation of interleukin-12 production / Regulated proteolysis of p75NTR / 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 / cellular response to interleukin-6 / Interleukin-1 processing / actinin binding / cellular response to angiotensin / interleukin-1-mediated signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / positive regulation of miRNA metabolic process / Fc-epsilon receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / TRAF6 mediated NF-kB activation / transcription factor binding / The NLRP3 inflammasome / Transcriptional Regulation by VENTX / positive regulation of type I interferon production / cellular response to interleukin-1 / Purinergic signaling in leishmaniasis infection / stress-activated MAPK cascade / nuclear pore / response to muscle stretch / NF-kB is activated and signals survival / CD209 (DC-SIGN) signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of NF-kappaB in B cells / RNA polymerase II transcription regulatory region sequence-specific DNA binding / TAK1-dependent IKK and NF-kappa-B activation / ISG15 antiviral mechanism / PKMTs methylate histone lysines / CLEC7A (Dectin-1) signaling / DNA-binding transcription repressor activity, RNA polymerase II-specific / negative regulation of inflammatory response / FCERI mediated NF-kB activation / Transcriptional regulation of white adipocyte differentiation / Interleukin-1 signaling / HCMV Early Events / cellular response to nicotine / cellular response to mechanical stimulus / protein import into nucleus / specific granule lumen / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / cellular response to tumor necrosis factor / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / gene expression / Senescence-Associated Secretory Phenotype (SASP) / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / secretory granule lumen / cellular response to lipopolysaccharide / 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 / 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 / enzyme binding / 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 / Domain of unknown function DUF3447 / 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 / Domain of unknown function DUF3447 / 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 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: 2.15 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
A: Importin subunit alpha-3
B: Isoform 3 of Nuclear factor NF-kappa-B p105 subunit


Theoretical massNumber of molelcules
Total (without water)55,3022
Polymers55,3022
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-5 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.751, 59.183, 86.239
Angle α, β, γ (deg.)90.000, 96.319, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 50325.812 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 BL21(DE3) (bacteria) / References: UniProt: O00629
#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: P19838-3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.2M potassium thiocyanate and 20% PEG3350

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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: Sep 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→85.72 Å / Num. obs: 26271 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 43.16 Å2 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.039 / Net I/σ(I): 13.4
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2043 / Rpim(I) all: 0.31

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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: 6BVZ

6bvz


Resolution: 2.15→48.7 Å / SU ML: 0.2738 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7566
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2616 1345 5.13 %
Rwork0.2257 24876 -
obs0.2275 26221 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 0 70 3354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023348
X-RAY DIFFRACTIONf_angle_d0.48234570
X-RAY DIFFRACTIONf_chiral_restr0.0356550
X-RAY DIFFRACTIONf_plane_restr0.0041594
X-RAY DIFFRACTIONf_dihedral_angle_d14.79971234
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.33631270.29522366X-RAY DIFFRACTION95.74
2.22-2.310.32551440.26522470X-RAY DIFFRACTION99.73
2.31-2.420.28881400.24162482X-RAY DIFFRACTION99.92
2.42-2.540.27511160.252507X-RAY DIFFRACTION99.73
2.54-2.70.32341410.27092478X-RAY DIFFRACTION99.81
2.7-2.910.32771340.26912479X-RAY DIFFRACTION99.89
2.91-3.210.25521000.25662537X-RAY DIFFRACTION99.96
3.21-3.670.29921410.25062497X-RAY DIFFRACTION99.92
3.67-4.620.22171470.19472493X-RAY DIFFRACTION100
4.62-48.70.22761550.18792567X-RAY DIFFRACTION99.82

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