7YYF image
Entry Detail
PDB ID:
7YYF
Keywords:
RNA BINDING PROTEIN
Title:
Orthorombic crystal structure of YTHDF1 YTH domain (G459N mutant) form II
Biological Source:
Source Organism:
Homo sapiens
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2022-02-17
Release Date:
2023-03-01
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.30 Å
R-Value Free:
0.21
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 21 21 21
7YYF validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:YTH domain-containing family protein 1
Mutations:First residue G derives from the expression tag: G459N
Chain IDs:A, B, C, D
Chain Length:200
Number of Molecules:4
Biological Source:Homo sapiens
UniProt ID:Q9BYJ9 Pfam ID:PF04146
Primary Citation
Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.
J.Chem.Inf.Model. ? ? ? (2024)
PMID: 38417111 DOI: 10.1021/acs.jcim.4c00051

Abstact

Epitranscriptomic mRNA modifications affect gene expression, with their altered balance detected in various cancers. YTHDF proteins contain the YTH reader domain recognizing the m6A mark on mRNA and represent valuable drug targets. Crystallographic structures have been determined for all three family members; however, discrepancies are present in the organization of the m6A-binding pocket. Here, we present new crystallographic structures of the YTH domain of YTHDF1, accompanied by computational studies, showing that this domain can exist in different stable conformations separated by a significant energetic barrier. During the transition, additional conformations are explored, with peculiar druggable pockets appearing and offering new opportunities for the design of YTH-interfering small molecules.

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Primary Citation of related structures
7YYE