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 1.3 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 60: 5932-5935

  • DOI: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YTH domain-containing family protein 3A [auth B],
B [auth A]
199Homo sapiensMutation(s): 0 
Gene Names: YTHDF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z739 (Homo sapiens)
Explore Q7Z739 
Go to UniProtKB:  Q7Z739
PHAROS:  Q7Z739
GTEx:  ENSG00000185728 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z739
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA5Homo sapiens
Sequence Annotations
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  • Reference Sequence
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

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_189363

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-28
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2021-01-13
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Database references, Refinement description