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- PDB-3tpo: Crystal structure of D192A/E396A mutant of mouse importin alpha2 -

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Basic information

Entry
Database: PDB / ID: 3tpo
TitleCrystal structure of D192A/E396A mutant of mouse importin alpha2
ComponentsImportin subunit alpha-2
KeywordsPROTEIN TRANSPORT / nuclear import
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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule ...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 / host cell / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / cytoplasmic stress granule / protein import into nucleus / histone deacetylase binding / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / nucleus / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHirano, H. / Matsuura, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Sensing actin dynamics: structural basis for G-actin-sensitive nuclear import of MAL
Authors: Hirano, H. / Matsuura, Y.
History
DepositionSep 8, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 1, 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

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Assembly

Deposited unit
A: Importin subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)57,8861
Polymers57,8861
Non-polymers00
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.343, 89.763, 99.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 57885.730 Da / Num. of mol.: 1 / Mutation: D192A, E396A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 0.1M HEPES, 1.0M KNa-tartrate, pH 7.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorDetector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→40.93 Å / Num. obs: 41730 / % possible obs: 99.8 %
Reflection shellResolution: 2.1→2.21 Å / % possible all: 98.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL

1ial


Resolution: 2.1→38.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.112 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1917 2115 5.1 %RANDOM
Rwork0.1596 ---
obs0.1612 41671 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.66 Å2 / Biso mean: 41.9304 Å2 / Biso min: 18.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---1.4 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 308 3650
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.023399
X-RAY DIFFRACTIONr_angle_refined_deg2.4191.9684627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5725.809136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.08815593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0741513
X-RAY DIFFRACTIONr_chiral_restr0.1720.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212497
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 146 -
Rwork0.276 2652 -
all-2798 -
obs--97.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.88295.50982.987910.49680.91956.9982-0.1158-0.24550.4584-0.6553-0.19911.05790.2876-0.7710.31490.17840.1352-0.14750.4069-0.26920.5262-2.465637.54916.5243
213.58641.00372.18887.1007-0.890411.9949-0.0595-0.09840.573-0.4306-0.01940.6197-0.2577-0.37660.07890.2510.05280.06750.0512-0.01950.15954.100961.87716.7853
34.53091.73840.69654.84783.12115.73750.04760.29680.1904-0.4479-0.12430.3445-0.1594-0.56120.07670.16490.04530.02660.09770.02960.09912.849154.860113.4328
41.8131-0.0596-0.44153.9160.46941.18710.0991-0.11090.06980.14120.0236-0.0588-0.0957-0.0316-0.12270.0184-0.00130.01070.0297-0.00640.01628.392740.592217.274
54.7395-0.3659-1.9382.5449-0.37354.1188-0.04820.0183-0.11350.09630.050.03730.0680.0154-0.00170.0472-0.0187-0.01590.019-0.00290.02922.292325.557215.2967
62.30430.0066-0.24733.94991.31013.49970.07220.0308-0.19420.12120.0378-0.0480.11050.0042-0.10990.0346-0.0183-0.03830.035-0.00390.0763-3.337816.58267.0027
72.5736-0.09430.5412.33460.96982.45540.01740.3347-0.0946-0.19850.0908-0.35590.00410.2668-0.10810.0414-0.00130.00090.1264-0.07090.1477-10.23318.8033-11.8984
82.92060.31131.71728.2439-1.4193.87970.09950.3842-0.3021-0.70240.0861-0.15460.22240.1589-0.18560.3790.02120.13330.5141-0.14670.3048-7.76482.6437-27.8108
90.77512.32560.089812.7791-1.95634.1205-0.28980.533-0.0318-1.02760.0378-0.7946-0.35410.60790.2520.6725-0.03270.15890.9563-0.08350.6102-0.65898.071-34.7353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 54
2X-RAY DIFFRACTION2A70 - 88
3X-RAY DIFFRACTION3A89 - 117
4X-RAY DIFFRACTION4A118 - 213
5X-RAY DIFFRACTION5A214 - 256
6X-RAY DIFFRACTION6A257 - 329
7X-RAY DIFFRACTION7A330 - 432
8X-RAY DIFFRACTION8A433 - 471
9X-RAY DIFFRACTION9A472 - 496

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