4R3I

The crystal structure of an RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 

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

  • 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 YTHD ...

    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]. chaor.xu@utoronto.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YTH domain-containing protein 1
A
166Homo sapiensGene Names: YTHDC1 (KIAA1966, YT521)
Find proteins for Q96MU7 (Homo sapiens)
Go to Gene View: YTHDC1
Go to UniProtKB:  Q96MU7
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3')B5synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6MZ
Query on 6MZ
B
RNA LINKINGC11 H16 N5 O7 PA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.728α = 90.00
b = 39.748β = 103.56
c = 56.238γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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