4IUF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.752 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids.

Kuo, P.H.Chiang, C.H.Wang, Y.T.Doudeva, L.G.Yuan, H.S.

(2014) Nucleic Acids Res. 42: 4712-4722

  • DOI: 10.1093/nar/gkt1407

  • PubMed Abstract: 
  • TDP-43 is an important pathological protein that aggregates in the diseased neuronal cells and is linked to various neurodegenerative disorders. In normal cells, TDP-43 is primarily an RNA-binding protein; however, how the dimeric TDP-43 binds RNA vi ...

    TDP-43 is an important pathological protein that aggregates in the diseased neuronal cells and is linked to various neurodegenerative disorders. In normal cells, TDP-43 is primarily an RNA-binding protein; however, how the dimeric TDP-43 binds RNA via its two RNA recognition motifs, RRM1 and RRM2, is not clear. Here we report the crystal structure of human TDP-43 RRM1 in complex with a single-stranded DNA showing that RRM1 binds the nucleic acid extensively not only by the conserved β-sheet residues but also by the loop residues. Mutational and biochemical assays further reveal that both RRMs in TDP-43 dimers participate in binding of UG-rich RNA or TG-rich DNA with RRM1 playing a dominant role and RRM2 playing a supporting role. Moreover, RRM1 of the amyotrophic lateral sclerosis-linked mutant D169G binds DNA as efficiently as the wild type; nevertheless, it is more resistant to thermal denaturation, suggesting that the resistance to degradation is likely linked to TDP-43 proteinopathies. Taken together all the data, we suggest a model showing that the two RRMs in each protomer of TDP-43 homodimer work together in RNA binding and thus the dimeric TDP-43 recognizes long clusters of UG-rich RNA to achieve high affinity and specificity.


    Organizational Affiliation

    Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsin Chu, Taiwan and Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taipei 10048, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TAR DNA-binding protein 43
A
77Homo 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
5'-D(*GP*TP*TP*GP*(XUA)P*GP*CP*GP*T)-3'B9N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
XUA
Query on XUA
B
DNA LINKINGC11 H16 N5 O6 P SeDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.752 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.110α = 90.00
b = 71.110β = 90.00
c = 101.663γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references