6ZOT

Crystal structure of YTHDF3 YTH domain in complex with m6A RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and Dynamic Insights into Redundant Function of YTHDF Proteins.

Li, Y.Bedi, R.K.Moroz-Omori, E.V.Caflisch, A.

(2020) J Chem Inf Model 

  • DOI: 10.1021/acs.jcim.0c01029
  • Primary Citation of Related Structures:  
    6ZOT

  • PubMed Abstract: 
  • Three YTH-domain family proteins (YTHDF1, YTHDF2, and YTHDF3) recognize the N 6 -methyladenosine (m 6 A) modification of mRNA in cells. However, the redundancy of their cellular functions has been disputed. We investigate their ...

    Three YTH-domain family proteins (YTHDF1, YTHDF2, and YTHDF3) recognize the N 6 -methyladenosine (m 6 A) modification of mRNA in cells. However, the redundancy of their cellular functions has been disputed. We investigate their interactions with m 6 A-containing RNA using X-ray crystallography and molecular dynamics (MD). The new X-ray structures and MD simulations show that the three proteins share identical interactions with the m 6 A-containing RNA and have similar intrinsic plasticity, thus evidencing the redundant roles of the three proteins in cellular functions.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YTH domain-containing family protein 3AB199Homo sapiensMutation(s): 0 
Gene Names: YTHDF3
Find proteins for Q7Z739 (Homo sapiens)
Explore Q7Z739 
Go to UniProtKB:  Q7Z739
NIH Common Fund Data Resources
PHAROS  Q7Z739
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNAC5Homo sapiens
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.70 Å
    • R-Value Free: 0.276 
    • R-Value Work: 0.215 
    • R-Value Observed: 0.218 
    • Space Group: P 4 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 100.75α = 90
    b = 100.75β = 90
    c = 72.88γ = 90
    Software Package:
    Software NamePurpose
    XDSdata reduction
    XSCALEdata scaling
    PHASERphasing
    PHENIXrefinement

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Swiss National Science FoundationSwitzerland310030B_189363

    Revision History 

    • Version 1.0: 2020-10-28
      Type: Initial release
    • Version 1.1: 2020-11-04
      Changes: Database references