› 4rcm

X-ray diffraction
1.8Å resolution

Crystal structure of the Pho92 YTH domain in complex with m6A

Released:
DOI: 10.2210/pdb4rcm/pdb
PDB entry 4rcm coloured by chain, front view.
PDB entry 4rcm coloured by chain, side view.
PDB entry 4rcm 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-170339 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Methylated RNA-binding protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 167 amino acids
Theoretical weight: 19.31 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q06390 (Residues: 141-306; Coverage: 54%)
Gene names: MRB1, PHO92, YDR374C
Sequence domains: YT521-B-like domain
Structure domains: ph1033 like domains
RNA (5'-R(*UP*G)-D(*(6MZ)P*CP*U)-3') Chains: D, E
Molecule details ›
Chains: D, E
Length: 5 nucleotides
Theoretical weight: 1.56 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand UNX 19 x UNX
1 modified residue:
Ligand 6MZ 2 x 6MZ

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E DW
Spacegroup: P21
Unit cell:
a: 41.43Å b: 57.171Å c: 66.725Å
α: 90° β: 103.08° γ: 90°
R-values:
R R work R free
0.22 0.218 0.268
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

57 review citations

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

6 mentions without citation

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