Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
Journal, issue, pages	Commun Biol, Vol. 2, Page 72, Year 2019
Publish date	Feb 20, 2019
Authors	Nai-Chi Chen / Masato Yoshimura / Naoyuki Miyazaki / Hong-Hsiang Guan / Phimonphan Chuankhayan / Chien-Chih Lin / Shao-Kang Chen / Pei-Ju Lin / Yen-Chieh Huang / Kenji Iwasaki / Atsushi Nakagawa / Sunney I Chan / Chun-Jung Chen /
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 ...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.
External links	Commun Biol / PubMed:30820467 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.17 - 3.7 Å
Structure data	6999 6ab5 EMDB-6999, PDB-6ab5: Cryo-EM structure of T=1 Penaeus vannamei nodavirus Method: EM (single particle) / Resolution: 3.7 Å 9576 6ab6 EMDB-9576, PDB-6ab6: Cryo-EM structure of T=3 Penaeus vannamei nodavirus Method: EM (single particle) / Resolution: 3.5 Å PDB-5yku: The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Zn ions Method: X-RAY DIFFRACTION / Resolution: 1.39 Å PDB-5ykv: The crystal structure of Macrobrachium rosenbergii nodavirus P-domain Method: X-RAY DIFFRACTION / Resolution: 2.31 Å PDB-5ykx: The crystal structure of Macrobrachium rosenbergii nodavirus P-domain with Cd ion Method: X-RAY DIFFRACTION / Resolution: 2.0 Å PDB-5ykz: The crystal structure of Penaeus vannamei nodavirus P-domain (P21) Method: X-RAY DIFFRACTION / Resolution: 1.17 Å PDB-5yl0: The crystal structure of Penaeus vannamei nodavirus P-domain (P212121) Method: X-RAY DIFFRACTION / Resolution: 1.22 Å PDB-5yl1: T=1 subviral particle of Penaeus vannamei nodavirus capsid protein deletion mutant (delta 1-37 & 251-368) Method: X-RAY DIFFRACTION / Resolution: 3.12 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-HOH: WATER / Water ChemComp-CD: Unknown entry ChemComp-EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH bufferYM / HEPES ChemComp-SO4: SULFATE ION / Sulfate ChemComp-CA*: Unknown entry
Source	penaeus vannamei nodavirus macrobrachium rosenbergii nodavirus
Keywords	VIRAL PROTEIN / Protrusion domain of viral capsid protein / viral capsid protein / VIRUS LIKE PARTICLE / Nodaviridae / shrimp nodavirus