4Y0F

Crystal Structure of Human TDP-43 RRM1 Domain in Complex with an Unmodified Single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.648 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation

Chiang, C.H.Grauffel, C.Wu, L.S.Kuo, P.H.Doudeva, L.G.Lim, C.Shen, C.K.Yuan, H.S.

(2016) Sci Rep 6: 21581-21581

  • DOI: 10.1038/srep21581
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The RNA-binding protein TDP-43 forms intracellular inclusions in amyotrophic lateral sclerosis (ALS). While TDP-43 mutations have been identified in ALS patients, how these mutations are linked to ALS remains unclear. Here we examined the biophysical ...

    The RNA-binding protein TDP-43 forms intracellular inclusions in amyotrophic lateral sclerosis (ALS). While TDP-43 mutations have been identified in ALS patients, how these mutations are linked to ALS remains unclear. Here we examined the biophysical properties of six ALS-linked TDP-43 mutants and found that one of the mutants, D169G, had higher thermal stability than wild-type TDP-43 and that it was cleaved by caspase 3 more efficiently, producing increased levels of the C-terminal 35 kD fragments (TDP-35) in vitro and in neuroblastoma cells. The crystal structure of the TDP-43 RRM1 domain containing the D169G mutation in complex with DNA along with molecular dynamics simulations reveal that the D169G mutation induces a local conformational change in a β turn and increases the hydrophobic interactions in the RRM1 core, thus enhancing the thermal stability of the RRM1 domain. Our results provide the first crystal structure of TDP-43 containing a disease-linked D169G mutation and a disease-related mechanism showing that D169G mutant is more susceptible to proteolytic cleavage by caspase 3 into the pathogenic C-terminal 35-kD fragments due to its increased stability in the RRM1 domain. Modulation of TDP-43 stability and caspase cleavage efficiency could present an avenue for prevention and treatment of TDP-43-linked neurodegeneration.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.,Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, 30013, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAR DNA-binding protein 43
A, B
103Homo sapiensMutation(s): 0 
Gene Names: TARDBP (TDP43)
Find proteins for Q13148 (Homo sapiens)
Go to Gene View: TARDBP
Go to UniProtKB:  Q13148
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*TP*GP*AP*GP*CP*GP*TP*T)-3')C,D10Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.648 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.240 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.027α = 90.00
b = 100.027β = 90.00
c = 98.144γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia SinicaTaiwan--
National Science CouncilTaiwan--

Revision History 

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Database references
  • Version 1.2: 2017-10-04
    Type: Derived calculations, Experimental preparation