› 4r3i

X-ray diffraction
1.8Å resolution

The crystal structure of an RNA complex

Released:
DOI: 10.2210/pdb4r3i/pdb
PDB entry 4r3i coloured by chain, front view.
PDB entry 4r3i coloured by chain, side view.
PDB entry 4r3i coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for selective binding of m6A RNA by the YTHDC1 YTH domain.
Xu C, Wang X, Liu K, Roundtree IA, Tempel W, Li Y, Lu Z, He C, Min J
Nat Chem Biol 10 927-9 (2014)
PMID: 25242552

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-188635 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
YTH domain-containing protein 1 Chain: A
Molecule details ›
Chain: A
Length: 166 amino acids
Theoretical weight: 18.82 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(*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: RIGAKU
Spacegroup: P21
Unit cell:
a: 35.728Å b: 39.748Å c: 56.238Å
α: 90° β: 103.56° γ: 90°
R-values:
R R work R free
0.206 0.203 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

155 review citations

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

20 mentions without citation

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