7N9H

Structure of the mammalian importin a1 bound to the TDP-43 NLS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Recognition of the TDP-43 nuclear localization signal by importin alpha 1/ beta.

Doll, S.G.Meshkin, H.Bryer, A.J.Li, F.Ko, Y.H.Lokareddy, R.K.Gillilan, R.E.Gupta, K.Perilla, J.R.Cingolani, G.

(2022) Cell Rep 39: 111007-111007

  • DOI: https://doi.org/10.1016/j.celrep.2022.111007
  • Primary Citation of Related Structures:  
    7N9H

  • PubMed Abstract: 

    Cytoplasmic mislocalization of the TAR-DNA binding protein of 43 kDa (TDP-43) leads to large, insoluble aggregates that are a hallmark of amyotrophic lateral sclerosis and frontotemporal dementia. Here, we study how importin α1/β recognizes TDP-43 bipartite nuclear localization signal (NLS). We find that the NLS makes extensive contacts with importin α1, especially at the minor NLS-binding site. NLS binding results in steric clashes with the C terminus of importin α1 that disrupts the TDP-43 N-terminal domain (NTD) dimerization interface. A putative phosphorylation site in the proximity of TDP-43 R83 at the minor NLS site destabilizes binding to importins by reducing the NLS backbone dynamics. Based on these data, we explain the pathogenic role of several post-translational modifications and mutations in the proximity of TDP-43 minor NLS site that are linked to disease and shed light on the chaperone activity of importin α1/β.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St., Philadelphia, PA 19107, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Importin subunit alpha-1A [auth C]428Homo sapiensMutation(s): 0 
Gene Names: KPNA2RCH1SRP1
UniProt & NIH Common Fund Data Resources
Find proteins for P52292 (Homo sapiens)
Explore P52292 
Go to UniProtKB:  P52292
PHAROS:  P52292
GTEx:  ENSG00000182481 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52292
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TAR DNA-binding protein 43B [auth A]24Homo sapiensMutation(s): 0 
Gene Names: TARDBPTDP43
UniProt & NIH Common Fund Data Resources
Find proteins for Q13148 (Homo sapiens)
Explore Q13148 
Go to UniProtKB:  Q13148
PHAROS:  Q13148
GTEx:  ENSG00000120948 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13148
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.373α = 90
b = 91.306β = 90
c = 97.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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 Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM140733
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: 2022-06-22
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-01-10
    Changes: Database references