The YTH domain of YTHDC1 protein in complex with GGm6AC oligonucleotide

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

Starting Model: experimental
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Flexible Binding of m6A Reader Protein YTHDC1 to Its Preferred RNA Motif.

Li, Y.Bedi, R.K.Wiedmer, L.Huang, D.Sledz, P.Caflisch, A.

(2019) J Chem Theory Comput 15: 7004-7014

  • DOI: https://doi.org/10.1021/acs.jctc.9b00987
  • Primary Citation of Related Structures:  
    6RT4, 6RT5, 6RT6, 6RT7

  • PubMed Abstract: 

    N 6 -Methyladenosine (m 6 A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m 6 A-containing RNAs to their readers are still elusive due to the unclear roles of m 6 A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G -2 G -1 (m 6 A)C +1 U +2 -3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m 6 A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Notably, simulations of unbound RNA motifs reveal that the methyl group of m 6 A and the 5' terminus shift the conformational preferences of the oligoribonucleotide to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m 6 A reader proteins.

  • Organizational Affiliation

    Department of Biochemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zurich , Switzerland.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
YTH domain-containing protein 1
B, C
166Homo sapiensMutation(s): 0 
Gene Names: YTHDC1KIAA1966YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens)
Explore Q96MU7 
Go to UniProtKB:  Q96MU7
GTEx:  ENSG00000083896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96MU7
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (5'-R(*(6MZ)P*C)-3')A,
D [auth E]
4Homo sapiens
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.913α = 90
b = 103.739β = 104.5
c = 41.983γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description