7LFC | pdb_00007lfc

Structure of importin a3 bound to p50 NLS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7LFC

This is version 1.2 of the entry. See complete history

Literature

Differential recognition of canonical NF-kappa B dimers by Importin alpha 3.

Florio, T.J.Lokareddy, R.K.Yeggoni, D.P.Sankhala, R.S.Ott, C.A.Gillilan, R.E.Cingolani, G.

(2022) Nat Commun 13: 1207-1207

  • DOI: https://doi.org/10.1038/s41467-022-28846-z
  • Primary Citation Related Structures: 
    7LEQ, 7LET, 7LEU, 7LF4, 7LFC

  • PubMed Abstract: 

    Nuclear translocation of the p50/p65 heterodimer is essential for NF-κB signaling. In unstimulated cells, p50/p65 is retained by the inhibitor IκBα in the cytoplasm that masks the p65-nuclear localization sequence (NLS). Upon activation, p50/p65 is translocated into the nucleus by the adapter importin α3 and the receptor importin β. Here, we describe a bipartite NLS in p50/p65, analogous to nucleoplasmin NLS but exposed in trans. Importin α3 accommodates the p50- and p65-NLSs at the major and minor NLS-binding pockets, respectively. The p50-NLS is the predominant binding determinant, while the p65-NLS induces a conformational change in the Armadillo 7 of importin α3 that stabilizes a helical conformation of the p65-NLS. Neither conformational change was observed for importin α1, which makes fewer bonds with the p50/p65 NLSs, explaining the preference for α3. We propose that importin α3 discriminates between the transcriptionally active p50/p65 heterodimer and p50/p50 and p65/65 homodimers, ensuring fidelity in NF-κB signaling.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA.

Macromolecule Content 

  • Total Structure Weight: 59.73 kDa 
  • Atom Count: 3,371 
  • Modeled Residue Count: 426 
  • Deposited Residue Count: 535 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit alpha-3521Homo sapiensMutation(s): 0 
Gene Names: KPNA4QIP1
UniProt & NIH Common Fund Data Resources
Find proteins for O00629 (Homo sapiens)
Explore O00629 
Go to UniProtKB:  O00629
PHAROS:  O00629
GTEx:  ENSG00000186432 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00629
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Nuclear factor NF-kappa-B p105 subunit14Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P19838 (Homo sapiens)
Explore P19838 
Go to UniProtKB:  P19838
PHAROS:  P19838
GTEx:  ENSG00000109320 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19838
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.220 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.65α = 90
b = 59.07β = 96.34
c = 86.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122844
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA56036
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesOD017987
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesOD023479

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description