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- PDB-3rzx: Mouse importin alpha-Ku70 NLS peptide complex -

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Basic information

Entry
Database: PDB / ID: 3rzx
TitleMouse importin alpha-Ku70 NLS peptide complex
Components
  • Importin subunit alpha-2
  • Ku70 NLS peptide
KeywordsPROTEIN TRANSPORT / Armadillo Repeats
Function / homology
Function and homology information


Ku70:Ku80 complex / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / Sensing of DNA Double Strand Breaks / DNA-dependent protein kinase-DNA ligase 4 complex / entry of viral genome into host nucleus through nuclear pore complex via importin / cellular response to X-ray / nonhomologous end joining complex / positive regulation of viral life cycle / DNA ligation ...Ku70:Ku80 complex / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / Sensing of DNA Double Strand Breaks / DNA-dependent protein kinase-DNA ligase 4 complex / entry of viral genome into host nucleus through nuclear pore complex via importin / cellular response to X-ray / nonhomologous end joining complex / positive regulation of viral life cycle / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / IRF3-mediated induction of type I IFN / host cell / recombinational repair / nuclear import signal receptor activity / nuclear localization sequence binding / cellular hyperosmotic salinity response / NLS-bearing protein import into nucleus / telomeric DNA binding / 2-LTR circle formation / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / DNA helicase activity / telomere maintenance / activation of innate immune response / cyclin binding / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / double-stranded DNA binding / scaffold protein binding / nuclear membrane / secretory granule lumen / DNA-binding transcription factor binding / ficolin-1-rich granule lumen / transcription regulator complex / postsynaptic density / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / innate immune response / negative regulation of DNA-templated transcription / glutamatergic synapse / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain ...Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta 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 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / 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 A-like domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
X-ray repair cross-complementing protein 6 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsTakeda, 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 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Ku70 NLS peptide


Theoretical massNumber of molelcules
Total (without water)57,8052
Polymers57,8052
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-1 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.518, 89.996, 100.142
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 / Fragment: NLS binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P52293
#2: Protein/peptide Ku70 NLS peptide


Mass: 2474.772 Da / Num. of mol.: 1 / Fragment: Nuclear localization signal / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12956
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.06 Å3/Da / Density % sol: 59.81 %
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: W01B-MX2 / Wavelength: 1.45859 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2008 / Details: SAGITALLY FOCUSED Si(111)
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45859 Å / Relative weight: 1
ReflectionResolution: 2.6→29.07 Å / Num. all: 22152 / Num. obs: 20974 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.9

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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
Starting model: PDB ENTRY 1PJN

1pjn


Resolution: 2.61→29.07 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.332 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22298 1129 5.1 %RANDOM
Rwork0.16762 ---
obs0.17041 20974 99.22 %-
all-22152 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.172 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.08 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.61→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 0 96 3373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0223336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3061.9684554
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3255437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.34625.76125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.50815549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2851511
X-RAY DIFFRACTIONr_chiral_restr0.1790.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022467
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.21728
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3460.22405
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0710.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6431.52210
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.27223523
X-RAY DIFFRACTIONr_scbond_it6.92231235
X-RAY DIFFRACTIONr_scangle_it9.9354.51031
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 77 -
Rwork0.282 1474 -
obs--96.52 %

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