5YKU

The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions

5YKU の概要

• エントリーDOI: 10.2210/pdb5yku/pdb
• 分子名称: Capsid protein, ZINC ION (3 entities in total)
• 機能のキーワード: protrusion domain of viral capsid protein, viral protein
• 由来する生物種: Macrobrachium rosenbergii nodavirus (MrNV)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 14076.61

構造登録者

Chen, N.C.,Yoshimura, M.,Lin, C.C.,Guan, H.H.,Chuankhayan, P.,Chen, C.J. (登録日: 2017-10-16, 公開日: 2018-10-24, 最終更新日: 2024-11-06)

主引用文献

Chen, N.C.,Yoshimura, M.,Miyazaki, N.,Guan, H.H.,Chuankhayan, P.,Lin, C.C.,Chen, S.K.,Lin, P.J.,Huang, Y.C.,Iwasaki, K.,Nakagawa, A.,Chan, S.I.,Chen, C.J.
The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Commun Biol, 2:72-72, 2019

PubMed Abstract: Shrimp nodaviruses, including (PvNV) and nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of  = 3 and  = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in  = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic -terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls  = 3 and  = 1 assemblies. Increasing the /-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.

PubMed: 30820467
DOI: 10.1038/s42003-019-0311-z

実験手法

X-RAY DIFFRACTION (1.39 Å)