› 4wqn

X-ray diffraction
2.12Å resolution

Crystal structure of N6-methyladenosine RNA reader YTHDF2

Released:
DOI: 10.2210/pdb4wqn/pdb
PDB entry 4wqn coloured by chain, front view.
PDB entry 4wqn coloured by chain, side view.
PDB entry 4wqn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the YTH domain of YTHDF2 reveals mechanism for recognition of N6-methyladenosine.
Zhu T, Roundtree IA, Wang P, Wang X, Wang L, Sun C, Tian Y, Li J, He C, Xu Y
Cell Res 24 1493-6 (2014)
PMID: 25412661

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195267 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain-containing family protein 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 173 amino acids
Theoretical weight: 19.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5A9 (Residues: 383-553; Coverage: 30%)
Gene names: HGRG8, YTHDF2
Sequence domains: YT521-B-like domain
Structure domains: ph1033 like domains

Ligands and Environments

2 bound ligands:
Ligand GOL 1 x GOL
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P65
Unit cell:
a: 76.689Å b: 76.689Å c: 131.241Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.221
Expression system: Escherichia coli

Quick links

Citations

79 review citations

Dynamic RNA Modifications in Gene Expression Regulation.
Roundtree et al. (2017)
78 more

3 mentions without citation

Structural Insights into N6-methyladenosine (m6A) Modification in the Transcriptome.
Huang et al. (2018)
2 more