|Entry||Database: PDB / ID: 6ab5|
|Title||Cryo-EM structure of T=1 Penaeus vannamei nodavirus|
|Keywords||VIRUS LIKE PARTICLE / Nodaviridae / shrimp nodavirus|
|Function / homology||Icosahedral viral capsid protein, S domain / Viral coat protein subunit / Viral coat protein (S domain) / viral capsid / structural molecule activity / Capsid protein|
Function and homology information
|Specimen source||Penaeus vannamei nodavirus|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å|
|Authors||Chen, N.C. / Miyazaki, N. / Yoshimura, M. / Guan, H.H. / Lin, C.C. / Iwasaki, K. / Chen, C.J.|
|Funding support||Taiwan , 1 items |
|Citation||Journal: Commun Biol / Year: 2019|
Title: The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism.
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 /
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.
SummaryFull reportAbout validation report
|Date||Deposition: Jul 20, 2018 / Release: Mar 20, 2019|
|Structure viewer||Molecule: |
Downloads & links
A: Capsid protein
A: Capsid proteinx 60
A: Capsid proteinx 5
A: Capsid proteinx 6
|#1: Protein/peptide|| |
Mass: 40262.168 Da / Num. of mol.: 1 / Source: (gene. exp.) Penaeus vannamei nodavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A5H7Q8
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Penaeus vannamei nodavirus / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT|
|Source (natural)||Organism: Penaeus vannamei nodavirus|
|Source (recombinant)||Organism: Escherichia coli (E. coli)|
|Details of virus||Empty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRUS-LIKE PARTICLE|
|Natural host||Organism: Litopenaeus vannamei|
|Buffer solution||pH: 7.4|
|Specimen||Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Grid material: MOLYBDENUM / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Cs: 0.01 mm / C2 aperture diameter: 100 microns / Alignment procedure: ZEMLIN TABLEAU|
|Specimen holder||Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 2 sec. / Electron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2806|
|Image scans||Width: 4096 / Height: 4096|
|Software||Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: I (icosahedral)|
|3D reconstruction||Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 70543 / Algorithm: FOURIER SPACE / Symmetry type: POINT|
|Refine LS restraints|
Refinement-ID: ELECTRON MICROSCOPY
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