4Y00

Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an Unmodified Single-stranded DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.266 

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 Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAR DNA-binding protein 43
A, B, C, D
103Homo sapiensMutation(s): 1 
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(P*TP*TP*GP*AP*GP*CP*GP*T)-3')E,F,G,H10Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.266 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 97.636α = 90.00
b = 97.636β = 90.00
c = 96.871γ = 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 Sinica, Taiwan, R.O.C.Taiwan--
National Science Council, Taiwan, R.O.C.Taiwan--

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