4XZR

Structure of yeast importin a bound to the membrane protein Nuclear Localization Signal sequence of INM protein Heh1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Distinctive Properties of the Nuclear Localization Signals of Inner Nuclear Membrane Proteins Heh1 and Heh2.

Lokareddy, R.K., Hapsari, R.A., van Rheenen, M., Pumroy, R.A., Bhardwaj, A., Steen, A., Veenhoff, L.M., Cingolani, G.

(2015) Structure 23: 1305-1316

  • DOI: https://doi.org/10.1016/j.str.2015.04.017
  • Primary Citation of Related Structures:  
    4PVZ, 4XZR

  • PubMed Abstract: 

    • Targeting of ER-synthesized membrane proteins to the inner nuclear membrane (INM) has long been explained by the diffusion-retention model. However, several INM proteins contain non-classical nuclear localization signal (NLS) sequences, which, in a few instances, have been shown to promote importin α/β- and Ran-dependent translocation to the INM ...

    Targeting of ER-synthesized membrane proteins to the inner nuclear membrane (INM) has long been explained by the diffusion-retention model. However, several INM proteins contain non-classical nuclear localization signal (NLS) sequences, which, in a few instances, have been shown to promote importin α/β- and Ran-dependent translocation to the INM. Here, using structural and biochemical methods, we show that yeast INM proteins Heh2 and Src1/Heh1 contain bipartite import sequences that associate intimately with the minor NLS-binding pocket of yeast importin α and unlike classical NLSs efficiently displace the IBB domain in the absence of importin β. In vivo, the intimate interactions at the minor NLS-binding pocket make the h2NLS highly efficient at recruiting importin α at the ER and drive INM localization of endogenous Heh2. Thus, h1/h2NLSs delineate a novel class of super-potent, IBB-like membrane protein NLSs, distinct from classical NLSs found in soluble cargos and of general interest in biology.

    Organizational Affiliation: 

    Dept. of Biochemistry and Molecular Biology, Thomas Jefferson University, 233 South 10 Street, Philadelphia, PA 19107, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inner nuclear membrane protein SRC154Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRC1, HEH1, YML034W, YML033W
UniProt
Find proteins for Q03707 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03707 
Go to UniProtKB:  Q03707
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03707
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Importin subunit alpha423Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SRP1, KAP60, YNL189W, N1606
UniProt
Find proteins for Q02821 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02821 
Go to UniProtKB:  Q02821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02821
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.682α = 90
b = 58.306β = 129.32
c = 95.372γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM074846

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence