+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0129 | |||||||||
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Title | Structure of the Macrobrachium rosenbergii Nodavirus | |||||||||
Map data | None | |||||||||
Sample |
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Keywords | Nodavirus / Capsid / Virion / VIRUS LIKE PARTICLE | |||||||||
Function / homology | Viral coat protein subunit / Capsid protein alpha Function and homology information | |||||||||
Biological species | Macrobrachium rosenbergii nodavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.28 Å | |||||||||
Authors | Ho KH / Gabrielsen M | |||||||||
Funding support | United Kingdom, 1 items
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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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0129.map.gz | 58.4 MB | EMDB map data format | |
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Header (meta data) | emd-0129-v30.xml emd-0129.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0129_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_0129.png | 260.5 KB | ||
Filedesc metadata | emd-0129.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0129 | HTTPS FTP |
-Validation report
Summary document | emd_0129_validation.pdf.gz | 265.5 KB | Display | EMDB validaton report |
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Full document | emd_0129_full_validation.pdf.gz | 264.6 KB | Display | |
Data in XML | emd_0129_validation.xml.gz | 16.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0129 | HTTPS FTP |
-Related structure data
Related structure data | 6h2bMC 0130C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10203 (Title: Structure of the Macrobrachium rosenbergii Nodavirus: A new genus within the Nodaviridae? Data size: 130.4 Data #1: Motion corrected micrographs of Macrobrachium rosenbergii nodavirus virus-like particles [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0129.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Macrobrachium rosenbergii nodavirus
Entire | Name: Macrobrachium rosenbergii nodavirus |
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Components |
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-Supramolecule #1: Macrobrachium rosenbergii nodavirus
Supramolecule | Name: Macrobrachium rosenbergii nodavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Capsid protein was expressed in Sf9 cells / NCBI-ID: 222557 / Sci species name: Macrobrachium rosenbergii nodavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Macrobrachium rosenbergii (giant freshwater prawn) |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Macrobrachium rosenbergii nodavirus |
Molecular weight | Theoretical: 41.563594 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MARGKQNSNQ AQNNSNANGK RRKRSRRNRN PQTIPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLTDSKSR ILVKQPISAS SFLGTRISGL SQFWERYRWH KAAVRYVPAV PNTLACQLIG YIDTDPLDDP NVILDVDQLL R QATSQVGA ...String: MARGKQNSNQ AQNNSNANGK RRKRSRRNRN PQTIPNFNPI VAKPTVAPLQ TNIRSARSDV NAITVLNGSD FLTTVKVRGS NNLTDSKSR ILVKQPISAS SFLGTRISGL SQFWERYRWH KAAVRYVPAV PNTLACQLIG YIDTDPLDDP NVILDVDQLL R QATSQVGA RQWNFSDTTT IPLIVRRDDQ LYYTGQDKEN VRFSQQGVFY LLQVTTLLNI SGEAITNDLI SGSLYLDWVC GF SMPQINP TPVEISQLTY NADTIGNWVP PTELNQTYTQ DITGLKPNSK FIIVPYMDRT SSEVLQKCTI TCNEVNAVGS ISY FDTNDI KCNGYITFQA NNIGEATFTL VTDYKGVTDA KPYQYRIIRA IVGNN UniProtKB: Capsid protein alpha |
-Macromolecule #2: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM HEPES, 100 mM NaCl pH 7.4 |
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K Details: VLPs were deposited onto a continuous carbon film that had been floated onto a quantifoil holey carbon film (R2/2). |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-20 / Number grids imaged: 1 / Number real images: 2459 / Average exposure time: 5.0 sec. / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
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. |
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Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 140 |
Output model | PDB-6h2b: |