ISDA

Entry Detail

PDB ID:

7YYJ

Keywords:

RNA BINDING PROTEIN

Title:

Tetragonal crystal structure of YTHDF1 YTH domain (544AVV546 mutant)

Biological Source:

Source Organism:

Homo sapiens

Host Organism:

Escherichia coli BL21(DE3)

PDB Version:

Deposition Date:

2022-02-18

Release Date:

2023-03-01

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.10 Å

R-Value Free:

0.22

R-Value Work:

0.19

R-Value Observed:

0.19

Space Group:

P 43 21 2

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:YTH domain-containing family protein 1
Mutations:First residue G derives from the expression tag: E544A/E545V/E546V
Chain IDs:A, B
Chain Length:200
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q9BYJ9 Pfam ID:PF04146

Ligand Molecules

EDO

SCN

Primary Citation

Pliability in the m 6 A-Binding Region Extends Druggability of YTH Domains.

Cazzanelli, G, Dalle Vedove, A, Spagnolli, G, Terruzzi, L, Colasurdo, E, Boldrini, A, Patsilinakos, A, Sturlese, M, Grottesi, A, Biasini, E, Provenzani, A, Quattrone, A, Lolli, G.Show

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