4WQN | pdb_00004wqn

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 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

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 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.
Medical Scientist Training Program and Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
1] Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA [2] Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA.

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 
• Modeled 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 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

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