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- PDB-4ba3: mImp_alphadIBB_A89NLS -

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Basic information

Entry
Database: PDB / ID: 4ba3
TitlemImp_alphadIBB_A89NLS
Components
  • A89NLS
  • IMPORTIN SUBUNIT ALPHA-2
KeywordsPROTEIN TRANSPORT/PEPTIDE / PROTEIN TRANSPORT-PEPTIDE COMPLEX
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 / 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)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
CitationJournal: Plant Cell / Year: 2012
Title: Crystal Structure of Rice Importin-Alpha and Structural Basis of its Interaction with Plant-Specific Nuclear Localization Signals.
Authors: Chang, C.-W. / Counago, R.L.M. / Williams, S.J. / Boden, M. / Kobe, B.
History
DepositionSep 11, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IMPORTIN SUBUNIT ALPHA-2
B: A89NLS


Theoretical massNumber of molelcules
Total (without water)55,1932
Polymers55,1932
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-1.7 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.829, 90.090, 99.427
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: 53672.695 Da / Num. of mol.: 1 / Fragment: NLS BINDING DOMAIN, RESIDUES 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET30A_MIMPALPHA_DIBB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52293
#2: Protein/peptide A89NLS


Mass: 1519.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PGEX2T-A89NLS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.2 Å3/Da / Density % sol: 61.54 % / Description: NONE
Crystal growDetails: 0.8 M SODIUM CITRATE, 0.1 M HEPES BUFFER, PH 6.5 AND 10 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.1→19.85 Å / Num. obs: 41996 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Biso Wilson estimate: 34.78 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 19.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 12.3 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAL

1ial


Resolution: 2.1→19.85 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.9352 / SU R Cruickshank DPI: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.125 / SU Rfree Cruickshank DPI: 0.124
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 2118 5.05 %RANDOM
Rwork0.1848 ---
obs0.1858 41937 100 %-
Displacement parametersBiso mean: 40.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.3734 Å20 Å20 Å2
2--7.751 Å20 Å2
3----7.3776 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 218 3527
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013367HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994584HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1569SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes475HARMONIC5
X-RAY DIFFRACTIONt_it3367HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion3.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion469SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4219SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2451 162 5.34 %
Rwork0.2135 2873 -
all0.215 3035 -
obs--100 %

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