Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

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This is version 2.0 of the entry. See complete history


Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.

Xu, C.Liu, K.Ahmed, H.Loppnau, P.Schapira, M.Min, J.

(2015) J Biol Chem 290: 24902-24913

  • DOI: https://doi.org/10.1074/jbc.M115.680389
  • Primary Citation of Related Structures:  
    4RCI, 4RCJ, 4RCM

  • PubMed Abstract: 

    N(6)-Methyladenosine (m(6)A) is the most abundant internal modification in RNA and is specifically recognized by YT521-B homology (YTH) domain-containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m(6)A nucleotide in RNA and preferentially binds to the GG(m(6)A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92 and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m(6)A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m(6)A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m(6)A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m(6)A nucleotide.

  • Organizational Affiliation

    From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7 and xuchaor@gmail.com.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YTH domain-containing family protein 1191Homo sapiensMutation(s): 0 
Gene Names: YTHDF1C20orf21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYJ9 (Homo sapiens)
Explore Q9BYJ9 
Go to UniProtKB:  Q9BYJ9
GTEx:  ENSG00000149658 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYJ9
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')5synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.648α = 90
b = 40.029β = 93.41
c = 59.308γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-09-09
    Changes: Database references
  • Version 1.2: 2015-10-21
    Changes: Database references
  • Version 2.0: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description