4WQN

Crystal structure of N6-methyladenosine RNA reader YTHDF2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine.

Zhu, T.Roundtree, I.A.Wang, P.Wang, X.Wang, L.Sun, C.Tian, Y.Li, J.He, C.Xu, Y.

(2014) Cell Res 24: 1493-1496


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YTH domain-containing family protein 2
A, B
173Homo sapiensMutation(s): 0 
Gene Names: YTHDF2HGRG8
Find proteins for Q9Y5A9 (Homo sapiens)
Go to UniProtKB:  Q9Y5A9
NIH Common Fund Data Resources
PHAROS  Q9Y5A9
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.689α = 90
b = 76.689β = 90
c = 131.241γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-19
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Database references