|Entry||Database: EMDB / ID: EMD-0129|
|Title||Structure of the Macrobrachium rosenbergii Nodavirus|
|Sample||Macrobrachium rosenbergii nodavirus:|
virus / Capsid proteinCapsid / ligand
|Function / homology||Viral coat protein subunit / Capsid protein|
Function and homology information
|Biological species||Macrobrachium rosenbergii nodavirus|
|Method||single particle reconstruction / cryo EM / Resolution: 3.28 Å|
|Authors||Ho KH / Gabrielsen M / Beh PL / Kueh CL / Thong QX / Streetley J / Tan WS / Bhella D|
|Funding support|| United Kingdom, 1 items |
|Citation||Journal: PLoS Biol. / Year: 2018|
Title: Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?
Authors: Kok Lian Ho / Mads Gabrielsen / Poay Ling Beh / Chare Li Kueh / Qiu Xian Thong / James Streetley / Wen Siang Tan / David Bhella /
Abstract: Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many ...Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.
|Validation Report||PDB-ID: 6h2b|
SummaryFull reportAbout validation report
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_0129.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.06 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Macrobrachium rosenbergii nodavirus
|Entire||Name: Macrobrachium rosenbergii nodavirus / Details: Capsid protein was expressed in Sf9 cells / Number of components: 3|
-Component #1: virus, Macrobrachium rosenbergii nodavirus
|Virus||Name: Macrobrachium rosenbergii nodavirus / Class: VIRUS-LIKE PARTICLE / Details: Capsid protein was expressed in Sf9 cells / Empty: No / Enveloped: No / Isolate: OTHER|
|Species||Species: Macrobrachium rosenbergii nodavirus|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
|Source (natural)||Host Species: Macrobrachium rosenbergii (giant freshwater prawn)|
|Shell #1||Name of element: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3|
-Component #2: protein, Capsid protein
|Protein||Name: Capsid proteinCapsid / Number of Copies: 3 / Recombinant expression: No|
|Mass||Theoretical: 41.563594 kDa|
|Source||Species: Macrobrachium rosenbergii nodavirus|
|Source (engineered)||Expression System: Spodoptera frugiperda (fall armyworm)|
-Component #3: ligand, CALCIUM ION
|Ligand||Name: CALCIUM IONCalcium / Number of Copies: 6 / Recombinant expression: No|
|Mass||Theoretical: 4.007805 MDa|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||Specimen conc.: 0.2 mg/mL / Buffer solution: 20 mM HEPES, 100 mM NaCl pH 7.4 / pH: 7.4|
|Vitrification||Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
Details: VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2).
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 36 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 47170.0 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm / Energy filter: GIF Bioquantum|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 QUANTUM (4k x 4k)|
|Image acquisition||Number of digital images: 2459|
-Atomic model buiding
|Modeling #1||Refinement space: REAL|
Details: Model built largely ab initio, following docking of a homology model based on PDB 4LLF. The homology model matched in two strands at residues - 104-135 and 232-243. This served as the starting point for manual model building. The model was then subjected to real space refinement using Phenix.
Overall bvalue: 140
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