› 4rcj

X-ray diffraction
1.6Å resolution

Crystal structure of YTHDF1 YTH domain in complex with 5mer m6A RNA

Released:
DOI: 10.2210/pdb4rcj/pdb
PDB entry 4rcj coloured by chain, front view.
PDB entry 4rcj coloured by chain, side view.
PDB entry 4rcj coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins.
Xu C, Liu K, Ahmed H, Loppnau P, Schapira M, Min J
J Biol Chem 290 24902-13 (2015)
PMID: 26318451

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189837 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
YTH domain-containing family protein 1 Chain: A
Molecule details ›
Chain: A
Length: 191 amino acids
Theoretical weight: 22.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9BYJ9 (Residues: 365-554; Coverage: 34%)
Gene names: C20orf21, YTHDF1
Sequence domains: YT521-B-like domain
Structure domains: ph1033 like domains
RNA (5'-R(*GP*GP*(6MZ)P*CP*U)-3') Chain: B
Molecule details ›
Chain: B
Length: 5 nucleotides
Theoretical weight: 1.6 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 7 x UNX
1 modified residue:
Ligand 6MZ 1 x 6MZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 37.648Å b: 40.029Å c: 59.308Å
α: 90° β: 93.41° γ: 90°
R-values:
R R work R free
0.173 0.171 0.21
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

52 review citations

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

16 mentions without citation

YTH Domain: A Family of N6-methyladenosine (m6A) Readers.
Liao et al. (2018)
15 more