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- PDB-5klt: Prototypical P4[M]cNLS -

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Basic information

Entry
Database: PDB / ID: 5klt
TitlePrototypical P4[M]cNLS
Components
  • Importin subunit alpha-1
  • Prototypical P4[M]cNLS
KeywordsPROTEIN TRANSPORT/Viral protein / Importin alpha / Complex / nuclear localisation signal / PROTEIN TRANSPORT-Viral protein 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 / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / 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 / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / host cell / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSmith, K.M. / Forwood, J.K.
CitationJournal: Biochim Biophys Acta Mol Cell Res / Year: 2018
Title: Contribution of the residue at position 4 within classical nuclear localization signals to modulating interaction with importins and nuclear targeting.
Authors: Smith, K.M. / Di Antonio, V. / Bellucci, L. / Thomas, D.R. / Caporuscio, F. / Ciccarese, F. / Ghassabian, H. / Wagstaff, K.M. / Forwood, J.K. / Jans, D.A. / Palu, G. / Alvisi, G.
History
DepositionJun 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
A: Prototypical P4[M]cNLS


Theoretical massNumber of molelcules
Total (without water)56,9652
Polymers56,9652
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 89.550, 99.769
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-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: 55268.473 Da / Num. of mol.: 1 / Fragment: UNp residues 70-529
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 Prototypical P4[M]cNLS


Mass: 1696.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 1M Sodium citrate pH6, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→26.7 Å / Num. obs: 22383 / % possible obs: 99.9 % / Redundancy: 14.1 % / Biso Wilson estimate: 34.34 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.3 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.7214.41.6131100
9.01-26.711.90.07196.4

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UL1

3ul1


Resolution: 2.6→26.698 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.18
RfactorNum. reflection% reflection
Rfree0.2281 1139 5.1 %
Rwork0.2066 --
obs0.2078 22331 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.09 Å2 / Biso mean: 44.5811 Å2 / Biso min: 19.17 Å2
Refinement stepCycle: final / Resolution: 2.6→26.698 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 0 0 3309
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023411
X-RAY DIFFRACTIONf_angle_d0.4954657
X-RAY DIFFRACTIONf_chiral_restr0.037563
X-RAY DIFFRACTIONf_plane_restr0.003595
X-RAY DIFFRACTIONf_dihedral_angle_d9.4232098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6002-2.71840.3521440.304226192763
2.7184-2.86160.2641370.270725782715
2.8616-3.04060.31071310.263426432774
3.0406-3.2750.24151530.25225992752
3.275-3.60390.24531410.22126222763
3.6039-4.12370.23091490.181926562805
4.1237-5.18920.1611510.157126672818
5.1892-26.69930.18641330.165828082941

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