Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.56 kDa 
• Atom Count: 3726 
• Modelled Residue Count: 447 
• Deposited Residue Count: 532 
• Unique protein chains: 2

3UL1

Mouse importin alpha: nucleoplasmin cNLS peptide complex

• PDB DOI: 10.2210/pdb3UL1/pdb

• Classification: PROTEIN TRANSPORT/NUCLEAR PROTEIN
• Organism(s): Mus musculus, Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-10 Released: 2012-10-03 
• Deposition Author(s): Marfori, M., Forwood, J.K., Lonhienne, T.G., Kobe, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Structural Basis of High-Affinity Nuclear Localization Signal Interactions with Importin-alpha

Marfori, M., Lonhienne, T.G., Forwood, J.K., Kobe, B.

(2012) Traffic 13: 532-548

• PubMed: 22248489 
• DOI: 10.1111/j.1600-0854.2012.01329.x
• Primary Citation of Related Structures:  
  3UKW, 3UKX, 3UKY, 3UKZ, 3UL0, 3UL1


• PubMed Abstract: 
  

Classical nuclear localization signals (cNLSs), comprising one (monopartite cNLSs) or two clusters of basic residues connected by a 10-12 residue linker (bipartite cNLSs), are recognized by the nuclear import factor importin-α. The cNLSs bind along a concave groove on importin-α; however, specificity determinants of cNLSs remain poorly understood. We present a structural and interaction analysis study of importin-α binding to both designed and naturally occurring high-affinity cNLS-like sequences; the peptide inhibitors Bimax1 and Bimax2, and cNLS peptides of cap-binding protein 80. Our data suggest that cNLSs and cNLS-like sequences can achieve high affinity through maximizing interactions at the importin-α minor site, and by taking advantage of multiple linker region interactions. Our study defines an extended set of binding cavities on the importin-α surface, and also expands on recent observations that longer linker sequences are allowed, and that long-range electrostatic complementarity can contribute to cNLS-binding affinity. Altogether, our study explains the molecular and structural basis of the results of a number of recent studies, including systematic mutagenesis and peptide library approaches, and provides an improved level of understanding on the specificity determinants of a cNLS. Our results have implications for identifying cNLSs in novel proteins.

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Organizational Affiliation: 

School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, 4072, Australia.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Importin subunit alpha-2	A [auth B]	510	Mus musculus	Mutation(s): 0  Gene Names: Kpna2, Rch1
UniProt & NIH Common Fund Data Resources
Find proteins for P52293 (Mus musculus) Explore P52293  Go to UniProtKB:  P52293
IMPC:  MGI:103561

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoplasmin	B [auth A]	22	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P05221 (Xenopus laevis) Explore P05221  Go to UniProtKB:  P05221

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.156	α = 90
b = 90.094	β = 90
c = 99.332	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-10 
• Released Date: 2012-10-03 
Deposition Author(s): Marfori, M., Forwood, J.K., Lonhienne, T.G., Kobe, B.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release