› 4rdn

X-ray diffraction
2.1Å resolution

Structure of YTH-YTHDF2 in complex with m6A

Released:
DOI: 10.2210/pdb4rdn/pdb
PDB entry 4rdn coloured by chain, front view.
PDB entry 4rdn coloured by chain, side view.
PDB entry 4rdn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the YTH domain of human YTHDF2 in complex with an m(6)A mononucleotide reveals an aromatic cage for m(6)A recognition.
Li F, Zhao D, Wu J, Shi Y
Cell Res 24 1490-2 (2014)
PMID: 25412658

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: 167 amino acids
Theoretical weight: 19.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y5A9 (Residues: 408-552; Coverage: 25%)
Gene names: HGRG8, YTHDF2
Sequence domains: YT521-B-like domain
Structure domains: ph1033 like domains

Ligands and Environments

2 bound ligands:
Ligand 6MD 2 x 6MD
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P65
Unit cell:
a: 80.73Å b: 80.73Å c: 113.48Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.217 0.27
Expression system: Escherichia coli

Quick links

Citations

56 review citations

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

11 mentions without citation

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