5YKU

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

Summary for 5YKU

• Entry DOI: 10.2210/pdb5yku/pdb
• Descriptor: Capsid protein, ZINC ION (3 entities in total)
• Functional Keywords: protrusion domain of viral capsid protein, viral protein
• Biological source: Macrobrachium rosenbergii nodavirus (MrNV)
• Total number of polymer chains: 1
• Total formula weight: 14076.61

Authors

Chen, N.C.,Yoshimura, M.,Lin, C.C.,Guan, H.H.,Chuankhayan, P.,Chen, C.J. (deposition date: 2017-10-16, release date: 2018-10-24, Last modification date: 2024-11-06)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.39 Å)