+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12879 | |||||||||
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Title | Structure of Alternanthera Mosaic VLP by cryoEM | |||||||||
Map data | Alternanthera mosaic VLP | |||||||||
Sample |
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Function / homology | Potexviruses and carlaviruses coat protein signature. / Potex/carlavirus coat protein / Viral coat protein / viral capsid / structural molecule activity / Coat protein Function and homology information | |||||||||
Biological species | Alternanthera mosaic virus | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Byrne MJ / Ranson NA / Lomonossoff GP / Thuenemann EC | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Viruses / Year: 2021 Title: A Replicating Viral Vector Greatly Enhances Accumulation of Helical Virus-Like Particles in Plants. Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan ...Authors: Eva C Thuenemann / Matthew J Byrne / Hadrien Peyret / Keith Saunders / Roger Castells-Graells / Inmaculada Ferriol / Mattia Santoni / John F C Steele / Neil A Ranson / Linda Avesani / Juan Jose Lopez-Moya / George P Lomonossoff / Abstract: The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient ...The production of plant helical virus-like particles (VLPs) via plant-based expression has been problematic with previous studies suggesting that an RNA scaffold may be necessary for their efficient production. To examine this, we compared the accumulation of VLPs from two potexviruses, papaya mosaic virus and alternanthera mosaic virus (AltMV), when the coat proteins were expressed from a replicating potato virus X- based vector (pEff) and a non-replicating vector (pEAQ-). Significantly greater quantities of VLPs could be purified when pEff was used. The pEff system was also very efficient at producing VLPs of helical viruses from different virus families. Examination of the RNA content of AltMV and tobacco mosaic virus VLPs produced from pEff revealed the presence of vector-derived RNA sequences, suggesting that the replicating RNA acts as a scaffold for VLP assembly. Cryo-EM analysis of the AltMV VLPs showed they had a structure very similar to that of authentic potexvirus particles. Thus, we conclude that vectors generating replicating forms of RNA, such as pEff, are very efficient for producing helical VLPs. | |||||||||
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_12879.map.gz | 30.5 MB | EMDB map data format | |
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Header (meta data) | emd-12879-v30.xml emd-12879.xml | 10.9 KB 10.9 KB | Display Display | EMDB header |
Images | emd_12879.png | 210.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12879 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12879 | HTTPS FTP |
-Related structure data
Related structure data | 7og6MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12879.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Alternanthera mosaic VLP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 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 : Alternanthera mosaic virus
Entire | Name: Alternanthera mosaic virus |
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Components |
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-Supramolecule #1: Alternanthera mosaic virus
Supramolecule | Name: Alternanthera mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 85454 / Sci species name: Alternanthera mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host system | Organism: Nicotiana benthamiana (plant) |
-Macromolecule #1: Coat protein
Macromolecule | Name: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Alternanthera mosaic virus |
Molecular weight | Theoretical: 22.243895 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MSTPFPQVTQ EQMNAFTPHT TSNLLPSPEQ LTTIANLLVA AKVPAASTTT IALELVNFCY DNGSSTYTAV VGPSSLAEVS LSQVANIVK ASGTSLRKFC RFFAPIIWNL RTDKTPPANW EANGFKPTEK FAAFDFFDGV ENPAAMQPPG GLVRTPSQAE R IANATNKQ ...String: MSTPFPQVTQ EQMNAFTPHT TSNLLPSPEQ LTTIANLLVA AKVPAASTTT IALELVNFCY DNGSSTYTAV VGPSSLAEVS LSQVANIVK ASGTSLRKFC RFFAPIIWNL RTDKTPPANW EANGFKPTEK FAAFDFFDGV ENPAAMQPPG GLVRTPSQAE R IANATNKQ VNLFQAAAQD NNFASNSAFI TKGQLSSNSP TIQYLPPPE |
-Macromolecule #2: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
Macromolecule | Name: RNA (5'-R(P*UP*UP*UP*UP*U)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Alternanthera mosaic virus |
Molecular weight | Theoretical: 1.485872 KDa |
Sequence | String: UUUUU |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 8 / Details: 10 mM Tris-HCl, pH 8.0 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 1.11 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final angle assignment | Type: NOT APPLICABLE |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 3.959 Å Applied symmetry - Helical parameters - Δ&Phi: 41.11 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 32018 |