6RT6

The YTH domain of YTHDC1 protein in complex with GGm6AC oligonucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.461 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif.

Li, Y.Bedi, R.K.Wiedmer, L.Huang, D.Sledz, P.Caflisch, A.

(2019) J Chem Theory Comput --: --

  • DOI: 10.1021/acs.jctc.9b00987
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • N6-methyladenosine (m <sup>6 </sup>A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m <s ...

    N6-methyladenosine (m 6 A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m 6 A-containing RNAs to their readers are still elusive due to the unclear roles of m 6 A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G -2 G -1 (m 6 A)C +1 U +2 -3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m 6 A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Moreover, simulations of unbound RNA motifs reveal that the methyl group of m 6 A and the 5' terminus shift the conformational preferences of the oligoribonucleotides to the bound-like conformation, thereby facilitating the association process. The binding mechanisms may help in the discovery of chemical probes against m 6 A reader proteins.



Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
YTH domain-containing protein 1
B, C
166Homo sapiensMutation(s): 0 
Gene Names: YTHDC1 (KIAA1966, YT521)
Find proteins for Q96MU7 (Homo sapiens)
Go to Gene View: YTHDC1
Go to UniProtKB:  Q96MU7
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*(6MZ)P*C)-3')A,E4Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MZ
Query on 6MZ
A, E
RNA LINKINGC11 H16 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.461 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.913α = 90.00
b = 103.739β = 104.50
c = 41.983γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release