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

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Basic information

Entry
Database: PDB / ID: 9clf
TitleImportin alpha isoform 2 with synthetic zero net-charge nuclear localization signal
Components
  • Importin subunit alpha-1
  • Zero net-charge NLS
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: 2.36 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 11, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,0888
Polymers57,5033
Non-polymers5855
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.398, 89.749, 99.523
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 NLS


Mass: 1086.257 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.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 59.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.65 M NaCit, 0.1 M HEPES pH 7.0, 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: 2.36→50 Å / Num. obs: 29674 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.039 / Rrim(I) all: 0.1 / Χ2: 0.765 / Net I/σ(I): 5.8 / Num. measured all: 190378
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.36-2.46.60.55814530.870.9640.2340.6060.396100
2.4-2.446.50.4614700.9280.9810.1950.5010.408100
2.44-2.496.40.41714560.9190.9790.1780.4540.446100
2.49-2.546.20.37814570.9330.9820.1660.4130.46100
2.54-2.660.34514420.9280.9810.1550.3790.442100
2.6-2.666.50.30214690.9550.9880.1290.3280.452100
2.66-2.726.60.27214800.9570.9890.1140.2950.522100
2.72-2.86.20.22214550.9670.9920.0970.2430.598100
2.8-2.886.30.20914550.970.9920.090.2280.599100
2.88-2.976.90.17514790.9810.9950.0710.1890.635100
2.97-3.086.90.15314630.9850.9960.0620.1650.689100
3.08-3.26.90.12814730.9920.9980.0530.1390.745100
3.2-3.356.80.11314840.9920.9980.0470.1230.813100
3.35-3.536.70.09714810.9930.9980.040.1050.97100
3.53-3.756.70.08114920.9950.9990.0340.0881.15100
3.75-4.036.50.07114700.9950.9990.030.0771.346100
4.03-4.446.10.0615100.9960.9990.0260.0651.308100
4.44-5.085.60.05315070.9970.9990.0250.0591.20199.9
5.08-6.45.90.05315470.9980.9990.0230.0580.959100
6.4-506.30.03616310.99910.0150.0391.144100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→49.81 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.531 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20778 1425 4.8 %RANDOM
Rwork0.15643 ---
obs0.15889 28194 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2---1.96 Å20 Å2
3---1.71 Å2
Refinement stepCycle: 1 / Resolution: 2.36→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 34 246 3644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123511
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163475
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.6434782
X-RAY DIFFRACTIONr_angle_other_deg0.4791.5728038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1825455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.897513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5910617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
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_it4.2464.3861781
X-RAY DIFFRACTIONr_mcbond_other4.244.3871781
X-RAY DIFFRACTIONr_mcangle_it6.3837.8552228
X-RAY DIFFRACTIONr_mcangle_other6.3827.8592229
X-RAY DIFFRACTIONr_scbond_it5.7235.1441730
X-RAY DIFFRACTIONr_scbond_other5.7225.1471731
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.9489.1152548
X-RAY DIFFRACTIONr_long_range_B_refined10.99553.1915361
X-RAY DIFFRACTIONr_long_range_B_other11.01352.9715163
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.36→2.419 Å
RfactorNum. reflection% reflection
Rfree0.251 98 -
Rwork0.223 2057 -
obs--99.77 %

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