› 7po6

X-ray diffraction
1.77Å resolution

Xist (m6A)UCG tetraloop RNA bound to the YTH domain of YTHDC1

Released:
DOI: 10.2210/pdb7po6/pdb
PDB entry 7po6 coloured by chain, front view.
PDB entry 7po6 coloured by chain, side view.
PDB entry 7po6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.
Jones AN, Tikhaia E, Mourão A, Sattler M
OpenAccess logo Nucleic Acids Res 50 2350-2362 (2022)
PMID: 35166835

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-188640 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
YTH domain-containing protein 1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 169 amino acids
Theoretical weight: 18.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96MU7 (Residues: 345-509; Coverage: 23%)
Gene names: KIAA1966, YT521, YTHDC1
Sequence domains: YT521-B-like domain
RNA (5'-R(*(6MZ)P*UP*C)-3') Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 14 nucleotides
Theoretical weight: 4.51 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand GTP 1 x GTP
Ligand EDO 7 x EDO
Ligand SO4 7 x SO4
Ligand NA 1 x NA
1 modified residue:
Ligand 6MZ 3 x 6MZ

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 78.438Å b: 85.119Å c: 88.617Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.2 0.232
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

m6A readers, writers, erasers, and the m6A epitranscriptome in breast cancer.
Petri et al. (2023)
6 more

1 mention without citation

Structural effects of m6A modification of the Xist A-repeat AUCG tetraloop and its recognition by YTHDC1.
Jones et al. (2022)