8IIB

Crystal structure of Israeli acute paralysis virus RNA-dependent RNA polymerase delta85 mutant (residues 86-546)

8IIB の概要

• エントリーDOI: 10.2210/pdb8iib/pdb
• 分子名称: Polymerase polyprotein, CADMIUM ION, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: rna-dependent rna polymerase, transferase
• 由来する生物種: Israeli acute paralysis virus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 110669.08

構造登録者

Fang, X.,Lu, G.,Hou, C.,Gong, P. (登録日: 2023-02-24, 公開日: 2023-06-07, 最終更新日: 2023-08-30)

主引用文献

Fang, X.,Lu, G.,Deng, Y.,Yang, S.,Hou, C.,Gong, P.
Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding.
Virol Sin, 38:531-540, 2023

PubMed Abstract: The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3D. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3D, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3D has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3D, namely Δ85 and Δ40, both missing the NE region, and the 3D protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3D structures are largely consistent with those of the PV 3D structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.

PubMed: 37156298
DOI: 10.1016/j.virs.2023.05.002

実験手法

X-RAY DIFFRACTION (2.69 Å)