› 4u8t

X-ray diffraction
2.7Å resolution

Crystal structure of YTH domain of Zygosaccharomyces rouxii MRB1 protein in complex with N6-Methyladenosine RNA

Released:
DOI: 10.2210/pdb4u8t/pdb
PDB entry 4u8t coloured by chain, front view.
PDB entry 4u8t coloured by chain, side view.
PDB entry 4u8t coloured by chain, top view.
Source organisms:
Primary publication:
Molecular basis for the recognition of methylated adenines in RNA by the eukaryotic YTH domain.
Luo S, Tong L
Proc Natl Acad Sci U S A 111 13834-9 (2014)
PMID: 25201973

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-111488 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
YTH domain-containing protein Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 177 amino acids
Theoretical weight: 20.54 KDa
Source organism: Zygosaccharomyces rouxii CBS 732
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C5E1V0 (Residues: 166-329; Coverage: 50%)
Gene name: ZYRO0G01672g
Sequence domains: YT521-B-like domain
Structure domains: ph1033 like domains
RNA (5'-R(*AP*GP*GP*(6MZ)P*CP*AP*U)-3') Chains: O, P, Q, R, S, T
Molecule details ›
Chains: O, P, Q, R, S, T
Length: 7 nucleotides
Theoretical weight: 2.26 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

No bound ligands
2 modified residues:
Ligand MSE 18 x MSE
Ligand 6MZ 6 x 6MZ

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P6122
Unit cell:
a: 117.39Å b: 117.39Å c: 380.928Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.201 0.199 0.245
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

58 review citations

Post-transcriptional gene regulation by mRNA modifications.
Zhao et al. (2017)
57 more

6 mentions without citation

Reading m6A in the Transcriptome: m6A-Binding Proteins.
Patil et al. (2018)
5 more