8YVB

Crystal structure of Caenorhabditis elegans ZIM-1 ZF1-2-CTD domain in complex with Chromosome II/III pairing center

8YVB の概要

• エントリーDOI: 10.2210/pdb8yvb/pdb
• 分子名称: C2H2-type domain-containing protein, DNA (5'-D(*TP*TP*GP*GP*TP*CP*TP*GP*CP*TP*A)-3'), DNA (5'-D(P*AP*GP*CP*AP*GP*AP*CP*CP*AP*A)-3'), ... (5 entities in total)
• 機能のキーワード: double stranded dna binding protein, dna binding protein
• 由来する生物種: Caenorhabditis elegans; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 21546.75

構造登録者

Li, F.D.,Li, M.L. (登録日: 2024-03-28, 公開日: 2024-12-11)

主引用文献

Li, M.,Zhu, C.,Xu, Z.,Xu, M.,Kuang, Y.,Hou, X.,Huang, X.,Lv, M.,Liu, Y.,Zhang, Y.,Xu, Z.,Han, X.,Wang, S.,Shi, Y.,Guang, S.,Li, F.
Structural basis for C. elegans pairing center DNA binding specificity by the ZIM/HIM-8 family proteins.
Nat Commun, 15:10355-10355, 2024

PubMed Abstract: Pairing center (PC) on each chromosome of Caenorhabditis elegans is crucial for homolog pairing and initiating synapsis. Within each PC, clusters of 11/12 bp DNA motif recruit one of four paralogous meiosis-specific proteins: ZIM-1, ZIM-2, ZIM-3, or HIM-8. However, the mechanistic basis underlying the specificity of ZIM/HIM-8-PC DNA interaction remains elusive. Here, we describe crystal structures of HIM-8, ZIM-1 and ZIM-2 DNA binding domains (ZF1, ZF2 and CTD) in complex with their cognate PC DNA motifs, respectively. These structures demonstrated the ZF1-2-CTD folds as an integrated structural unit crucial for its DNA binding specificity. Base-specific DNA-contacting residues are exclusively distributed on ZF1-2 and highly conserved. Furthermore, the CTD potentially contributes to the conformational diversity of ZF1-2, imparting binding specificity to distinct PC DNA motifs. These findings shed light on the mechanism governing PC DNA motif recognition by ZIM/HIM-8 proteins, suggesting a co-evolution relationship between PC DNA motifs and ZF1-2-CTD in shaping the specific recognition.

PubMed: 39609407
DOI: 10.1038/s41467-024-54548-9

実験手法

X-RAY DIFFRACTION (1.9 Å)