3ZIP

minor-site specific NLS (A58)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Distinctive Conformation of Minor Site-Specific Nuclear Localization Signals Bound to Importin-Alpha

Chang, C.-W.Counago, R.M.Williams, S.J.Boden, M.Kobe, B.

(2013) Traffic 14: 1144

  • DOI: https://doi.org/10.1111/tra.12098
  • Primary Citation of Related Structures:  
    3ZIN, 3ZIO, 3ZIP, 3ZIQ, 3ZIR

  • PubMed Abstract: 

    Nuclear localization signals (NLSs) contain one or two clusters of basic residues and are recognized by the import receptor importin-α. There are two NLS-binding sites (major and minor) on importin-α and the major NLS-binding site is considered to be the primary binding site. Here, we used crystallographic and biochemical methods to investigate the binding between importin-α and predicted 'minor site-specific' NLSs: four peptide library-derived peptides, and the NLS from mouse RNA helicase II/Guα. The crystal structures reveal that these atypical NLSs indeed preferentially bind to the minor NLS-binding site. Unlike previously characterized NLSs, the C-terminal residues of these NLSs form an α-helical turn, stabilized by internal H-bond and cation-π interactions between the aromatic residues from the NLSs and the positively charged residues from importin-α. This helical turn sterically hinders binding at the major NLS-binding site, explaining the minor-site preference. Our data suggest the sequence RXXKR[K/X][F/Y/W]XXAF as the optimal minor NLS-binding site-specific motif, which may help identify novel proteins with atypical NLSs.


  • Organizational Affiliation

    School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld, 4072, Australia; Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Qld, 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMPORTIN SUBUNIT ALPHA-2461Mus musculusMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus)
Explore P52293 
Go to UniProtKB:  P52293
IMPC:  MGI:103561
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52293
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
A58NLS
B, C
12synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.14α = 90
b = 90.18β = 90
c = 99.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-10-30
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description