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 

Starting Model: experimental
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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