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- PDB-9cl8: Importin alpha isoform 2 with synthetic zero net-charge nuclear l... -

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Basic information

Entry
Database: PDB / ID: 9cl8
TitleImportin alpha isoform 2 with synthetic zero net-charge nuclear localization signal
Components
  • Importin subunit alpha-1
  • Zero net-charge nuclear localization signal
KeywordsPROTEIN TRANSPORT / Nuclear transport / nuclear localization signal binding / ARM repeats
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
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 ...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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsZeytuni, N. / Yang, Z. / Odeh-Ahmed, A. / Abdoli, A. / Leyton, V.J. / Bednova, O. / Lavigne, P. / Lemieux, B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Other government Canada
CitationJournal: Protein Sci. / Year: 2025
Title: Probing the extent of importin-alpha targeting of the TAF8 NLS by eliminating its cationic net-charge.
Authors: Abdoli, A. / Yang, Z. / Odeh-Ahmed, A. / Bednova, O. / Lemieux, B. / Dawe, L. / Ravel-Chapuis, A. / Lavigne, P. / Zeytuni, N. / Leyton, J.V.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit alpha-1
C: Zero net-charge nuclear localization signal
B: Zero net-charge nuclear localization signal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0308
Polymers57,5073
Non-polymers5235
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-7 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.411, 89.698, 99.424
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-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: 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52293
#2: Protein/peptide Zero net-charge nuclear localization signal / Zero net-charge NLS


Mass: 1088.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.8 M NaCit, 0.1M HEPES pH 6.4, 60% glycerol, 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 41131 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Χ2: 0.63 / Net I/σ(I): 6.3 / Num. measured all: 270049
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.11-2.156.90.50120110.9010.9740.2050.5420.381100
2.15-2.196.90.44120490.9380.9840.1810.4770.382100
2.19-2.236.90.37619970.950.9870.1540.4070.397100
2.23-2.276.80.31520310.9530.9880.130.3410.445100
2.27-2.326.80.27720340.9690.9920.1140.30.437100
2.32-2.386.70.26420340.9660.9910.110.2870.439100
2.38-2.446.60.21820410.980.9950.0920.2370.47100
2.44-2.56.50.19220100.980.9950.0820.2090.496100
2.5-2.586.10.17120490.9830.9960.0750.1870.495100
2.58-2.666.40.15620280.9860.9960.0660.170.545100
2.66-2.756.50.1320340.9890.9970.0550.1410.574100
2.75-2.866.20.1120560.9910.9980.0480.120.606100
2.86-2.996.90.09820510.9930.9980.040.1060.671100
2.99-3.156.90.08220510.9960.9990.0340.0890.745100
3.15-3.356.90.07120590.9970.9990.0290.0760.816100
3.35-3.616.70.06120730.9970.9990.0250.0670.977100
3.61-3.976.60.05220750.9980.9990.0220.0571.075100
3.97-4.546.20.04520900.9980.9990.020.0491.071100
4.54-5.725.60.0421150.99810.0180.0440.867100
5.72-506.30.02922430.99910.0130.0320.75299.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→49.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.568 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19156 2047 5 %RANDOM
Rwork0.1595 ---
obs0.16116 39023 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å2-0 Å2
2---2.11 Å20 Å2
3---1.84 Å2
Refinement stepCycle: 1 / Resolution: 2.11→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 32 313 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123464
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163434
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.6384724
X-RAY DIFFRACTIONr_angle_other_deg0.5341.5717939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7485453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.771512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95510609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023990
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02700
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0213.8831759
X-RAY DIFFRACTIONr_mcbond_other4.023.8841759
X-RAY DIFFRACTIONr_mcangle_it5.5266.9532199
X-RAY DIFFRACTIONr_mcangle_other5.5266.9562200
X-RAY DIFFRACTIONr_scbond_it5.5934.5991705
X-RAY DIFFRACTIONr_scbond_other5.5924.6021706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4568.1222515
X-RAY DIFFRACTIONr_long_range_B_refined10.42349.4515597
X-RAY DIFFRACTIONr_long_range_B_other10.42448.915292
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.163 Å
RfactorNum. reflection% reflection
Rfree0.245 145 -
Rwork0.219 2775 -
obs--97.89 %

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