4WQN

Crystal structure of N6-methyladenosine RNA reader YTHDF2

• PDB DOI: https://doi.org/10.2210/pdb4WQN/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-10-22 Released: 2014-11-19 
• Deposition Author(s): Zhu, T., Roundtree, I.A., Wang, P., Wang, X., Wang, L., Sun, C., Tian, Y., Li, J., He, C., Xu, Y.

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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 

Starting Model: experimental

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

• PubMed: 25412661 
• DOI: https://doi.org/10.1038/cr.2014.152
• Primary Citation of Related Structures:  
  4WQN

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Organizational Affiliation: 

Fudan University Shanghai Cancer Center, Department of Oncology; and Institute of Biomedical Sciences and School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.19 kDa 
• Atom Count: 2,667 
• Modelled Residue Count: 302 
• Deposited Residue Count: 346 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YTH domain-containing family protein 2	A, B	173	Homo sapiens	Mutation(s): 0  Gene Names: YTHDF2, HGRG8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5A9 (Homo sapiens) Explore Q9Y5A9  Go to UniProtKB:  Q9Y5A9
PHAROS:  Q9Y5A9 GTEx:  ENSG00000198492

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth B], E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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 = 76.689	α = 90
b = 76.689	β = 90
c = 131.241	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Zhu, T., Roundtree, I.A., Wang, P., Wang, X., Wang, L., Sun, C., Tian, Y., Li, J., He, C., Xu, Y.

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2014-12-10
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy