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- PDB-3rz9: Mouse importin alpha-Ku80 NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 3rz9
TitleMouse importin alpha-Ku80 NLS peptide complex
Components
  • Importin subunit alpha-2
  • Ku80 NLS peptide
KeywordsPROTEIN TRANSPORT / Armadillo repeat
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / Sensing of DNA Double Strand Breaks / small-subunit processome assembly / regulation of transcription by glucose / entry of viral genome into host nucleus through nuclear pore complex via importin / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / positive regulation of viral life cycle ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / Sensing of DNA Double Strand Breaks / small-subunit processome assembly / regulation of transcription by glucose / entry of viral genome into host nucleus through nuclear pore complex via importin / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / regulation of smooth muscle cell proliferation / postsynapse to nucleus signaling pathway / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / IRF3-mediated induction of type I IFN / U3 snoRNA binding / nuclear import signal receptor activity / NLS-bearing protein import into nucleus / regulation of telomere maintenance / nuclear localization sequence binding / recombinational repair / non-canonical NF-kappaB signal transduction / protein localization to chromosome, telomeric region / 2-LTR circle formation / telomeric repeat DNA binding / DNA 3'-5' helicase / 3'-5' DNA helicase activity / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / positive regulation of type I interferon production / activation of innate immune response / telomere maintenance / protein import into nucleus / DNA helicase activity / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / site of DNA damage / cellular response to gamma radiation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / protein-DNA complex / double-strand break repair via nonhomologous end joining / enzyme activator activity / histone deacetylase binding / cytoplasmic stress granule / double-strand break repair / host cell / nuclear membrane / double-stranded DNA binding / DNA recombination / secretory granule lumen / DNA-binding transcription factor binding / damaged DNA binding / chromosome, telomeric region / postsynaptic density / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / Neutrophil degranulation / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / protein-containing complex binding / glutamatergic synapse / ATP hydrolysis activity / protein-containing complex / DNA binding / DNA-templated transcription / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen ...Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal 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 / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Alpha Horseshoe / Armadillo-like helical / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA repair protein Ku80 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsBarros, A.C. / Takeda, A.A.S. / Fontes, M.R.M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural basis of importin-alpha-mediated nuclear transport for Ku70 and Ku80.
Authors: Takeda, A.A. / de Barros, A.C. / Chang, C.W. / Kobe, B. / Fontes, M.R.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-2
B: Ku80 NLS peptide


Theoretical massNumber of molelcules
Total (without water)56,7782
Polymers56,7782
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-3 kcal/mol
Surface area17490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.357, 88.295, 98.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Importin subunit alpha-2 / 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: 55330.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P52293
#2: Protein/peptide Ku80 NLS peptide


Mass: 1447.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P13010
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.43 Å / Relative weight: 1
ReflectionResolution: 2.29→26.49 Å / Num. all: 29010 / Num. obs: 27469 / % possible obs: 98.71 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.29→2.349 Å / % possible all: 98.71

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→26.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.11 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21797 1541 5 %RANDOM
Rwork0.17747 ---
obs0.17952 27469 98.71 %-
all-29010 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.086 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.29→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 0 216 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223356
X-RAY DIFFRACTIONr_angle_refined_deg1.9841.974576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1745435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.47425.859128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76815570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1571511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022463
X-RAY DIFFRACTIONr_nbd_refined0.2320.22046
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.215
X-RAY DIFFRACTIONr_mcbond_it1.1711.52210
X-RAY DIFFRACTIONr_mcangle_it2.14823518
X-RAY DIFFRACTIONr_scbond_it3.37731264
X-RAY DIFFRACTIONr_scangle_it5.354.51058
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.516 103 -
Rwork0.344 1887 -
obs--88.44 %

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