› 6zd7

X-ray diffraction
1.75Å resolution

Crystal structure of YTHDC1 T379V mutant complex with m6A

Released:
DOI: 10.2210/pdb6zd7/pdb
PDB entry 6zd7 coloured by chain, front view.
PDB entry 6zd7 coloured by chain, side view.
PDB entry 6zd7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m6A) Recognition by the Reader Domain of YTHDC1.
Li Y, Bedi RK, Wiedmer L, Sun X, Huang D, Caflisch A
J Chem Theory Comput 17 1240-1249 (2021)
PMID: 33472367

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-167928 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
YTH domain containing 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 183 amino acids
Theoretical weight: 20.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand SO4 7 x SO4
Ligand 6MD 2 x 6MD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P21
Unit cell:
a: 40.01Å b: 104Å c: 41.91Å
α: 90° β: 105.323° γ: 90°
R-values:
R R work R free
0.208 0.207 0.238
Expression system: Escherichia coli

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Citations

3 review citations

RNA N6-Methyladenosine Modifications and Its Roles in Alzheimer's Disease.
Zhang et al. (2022)
2 more