4R3I

The crystal structure of an RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for selective binding of m(6)A RNA by the YTHDC1 YTH domain.

Xu, C.Wang, X.Liu, K.Roundtree, I.A.Tempel, W.Li, Y.Lu, Z.He, C.Min, J.

(2014) Nat Chem Biol 10: 927-929

  • DOI: 10.1038/nchembio.1654
  • Primary Citation of Related Structures:  
    4R3H, 4R3I

  • PubMed Abstract: 
  • N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA ...

    N(6)-methyladenosine (m(6)A) is the most abundant internal modification of nearly all eukaryotic mRNAs and has recently been reported to be recognized by the YTH domain family proteins. Here we present the crystal structures of the YTH domain of YTHDC1, a member of the YTH domain family, and its complex with an m(6)A-containing RNA. Our structural studies, together with transcriptome-wide identification of YTHDC1-binding sites and biochemical experiments, not only reveal the specific mode of m(6)A-YTH binding but also explain the preferential recognition of the GG(m(6)A)C sequences by YTHDC1.


    Organizational Affiliation

    1] Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. [2] Department of Physiology, University of Toronto, Toronto, Ontario, Canada.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YTH domain-containing protein 1A166Homo sapiensMutation(s): 0 
Gene Names: YTHDC1KIAA1966YT521
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU7 (Homo sapiens)
Explore Q96MU7 
Go to UniProtKB:  Q96MU7
PHAROS:  Q96MU7
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')B5synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 35.728α = 90
    b = 39.748β = 103.56
    c = 56.238γ = 90
    Software Package:
    Software NamePurpose
    Aimlessdata scaling
    PHASERphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    XDSdata reduction

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2014-09-17
      Type: Initial release
    • Version 1.1: 2014-10-01
      Changes: Database references
    • Version 1.2: 2014-11-19
      Changes: Database references