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Yorodumi- EMDB-11911: Nudaurelia capensis omega virus procapsid: virus-like particles e... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11911 | ||||||||||||
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Title | Nudaurelia capensis omega virus procapsid: virus-like particles expressed in Nicotiana benthamiana | ||||||||||||
Map data | Density improved map from phenix.resolve_cryo_em at 6.63 Ang resolution | ||||||||||||
Sample |
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Function / homology | Peptidase N2 / Peptidase family A21 / Viral coat protein subunit / p70 Function and homology information | ||||||||||||
Biological species | Nudaurelia capensis omega virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.63 Å | ||||||||||||
Authors | Castells-Graells R / Ribeiro JRS / Domitrovic T / Hesketh EL / Scarff CA / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Commun Biol / Year: 2021 Title: Plant-expressed virus-like particles reveal the intricate maturation process of a eukaryotic virus. Authors: Roger Castells-Graells / Jonas R S Ribeiro / Tatiana Domitrovic / Emma L Hesketh / Charlotte A Scarff / John E Johnson / Neil A Ranson / David M Lawson / George P Lomonossoff / Abstract: Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus ...Many virus capsids undergo exquisitely choreographed maturation processes in their host cells to produce infectious virions, and these remain poorly understood. As a tool for studying virus maturation, we transiently expressed the capsid protein of the insect virus Nudaurelia capensis omega virus (NωV) in Nicotiana benthamiana and were able to purify both immature procapsids and mature capsids from infiltrated leaves by varying the expression time. Cryo-EM analysis of the plant-produced procapsids and mature capsids to 6.6 Å and 2.7 Å resolution, respectively, reveals that in addition to large scale rigid body motions, internal regions of the subunits are extensively remodelled during maturation, creating the active site required for autocatalytic cleavage and infectivity. The mature particles are biologically active in terms of their ability to lyse membranes and have a structure that is essentially identical to authentic virus. The ability to faithfully recapitulate and visualize a complex maturation process in plants, including the autocatalytic cleavage of the capsid protein, has revealed a ~30 Å translation-rotation of the subunits during maturation as well as conformational rearrangements in the N and C-terminal helical regions of each subunit. | ||||||||||||
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_11911.map.gz | 40.7 MB | EMDB map data format | |
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Header (meta data) | emd-11911-v30.xml emd-11911.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11911_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_11911.png | 228.7 KB | ||
Masks | emd_11911_msk_1.map | 103 MB | Mask map | |
Others | emd_11911_additional_1.map.gz emd_11911_half_map_1.map.gz emd_11911_half_map_2.map.gz | 96 MB 80 MB 80 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11911 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11911 | HTTPS FTP |
-Related structure data
Related structure data | 7ataMC 7anmC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10555 (Title: Nudaurelia capensis omega virus procapsid: virus-like particles expressed in Nicotiana benthamiana Data size: 1.0 TB Data #1: aligned and dose-weighted micrographs [micrographs - single frame] Data #2: aligned and non-dose-weighted micrographs [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11911.map.gz / Format: CCP4 / Size: 43.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Density improved map from phenix.resolve_cryo_em at 6.63 Ang resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11911_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Postprocessed map from Relion at 7.1 Ang resolution
File | emd_11911_additional_1.map | ||||||||||||
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Annotation | Postprocessed map from Relion at 7.1 Ang resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half map 1 from Relion at 7.52 Ang resolution
File | emd_11911_half_map_1.map | ||||||||||||
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Annotation | Refine3D half map 1 from Relion at 7.52 Ang resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half map 2 from Relion at 7.52 Ang resolution
File | emd_11911_half_map_2.map | ||||||||||||
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Annotation | Refine3D half map 2 from Relion at 7.52 Ang resolution | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Nudaurelia capensis omega virus
Entire | Name: Nudaurelia capensis omega virus |
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Components |
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-Supramolecule #1: Nudaurelia capensis omega virus
Supramolecule | Name: Nudaurelia capensis omega virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The codon-optimized sequence was transiently expressed in Nicotiana benthamiana NCBI-ID: 12541 / Sci species name: Nudaurelia capensis omega virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Gonimbrasia cytherea (butterflies/moths) |
Host system | Organism: Nicotiana benthamiana (plant) / Recombinant cell: leaf tissue / Recombinant plasmid: pEAQ-HT |
Molecular weight | Theoretical: 16.76 MDa |
Virus shell | Shell ID: 1 / Name: coat / Diameter: 480.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: p70
Macromolecule | Name: p70 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Nudaurelia capensis omega virus |
Molecular weight | Theoretical: 62.094828 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MDSNSASGKR RSRNVRIAAN TVNVAPKQRQ ARGRRARSRA NNIDNVTAAA QELGQSLDAN VITFPTNVAT MPEFRSWARG KLDIDQDSI GWYFKYLDPA GATESARAVG EYSKIPDGLV KFSVDAEIRE IYNEECPTVS DASIPLDGAQ WSLSIISYPM F RTAYFAVA ...String: MDSNSASGKR RSRNVRIAAN TVNVAPKQRQ ARGRRARSRA NNIDNVTAAA QELGQSLDAN VITFPTNVAT MPEFRSWARG KLDIDQDSI GWYFKYLDPA GATESARAVG EYSKIPDGLV KFSVDAEIRE IYNEECPTVS DASIPLDGAQ WSLSIISYPM F RTAYFAVA NVDNKEISLD VTNDLIVWLN NLASWRDVVD SGQWFTFSDD PTWFVRIRVL HPTYDLPDPT EGLLRTVSDY RL TYKSITC EANMPTLVDQ GFWIGGHYAL TPIATTQNAV EGSGFVHPFN VTRPGIAAGV TLTWASMPPG GSAPSGDPAW IPD STTQFQ WRHGGFDAPT GVITYTIPRG YTMQYFDTTT NEWNGFANPD DVVTFGQTGG AAGTNATITI TAPTVTLTIL ATTT SAANV INFRNLDAET TAASNRSEVP LPPLTFGQTA PNNPKIEQTL VKDTLGSYLV HSKMRNPVFQ LTPASSFGAI SFTNP GFDR NLDLPGFGGI RDSLDVNMST AVCHFRSLSK SCSIVTKTYQ GWEGVTNVNT PFGQFAHSGL LKNDEILCLA DDLATR LTG VYGATDN |
-Macromolecule #2: p70
Macromolecule | Name: p70 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Nudaurelia capensis omega virus |
Molecular weight | Theoretical: 7.815102 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: FAAAVLAFAA NMLTSVLKSE ATTSVIKELG NQATGLANQG LARLPGLLAS IPGKIAARVR ARRDRRRAAR MNNN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.6 |
Grid | Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / 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 | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 75000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 8554 / Average exposure time: 1.5 sec. / Average electron dose: 72.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | The model was built and refined against a density modified map generated using phenix.resolve_cryo_em. This used the Relion half maps as inputs and improved the resolution to 6.6 Angstrom. |
Refinement | Space: REAL / Protocol: OTHER / Overall B value: 105.8 / Target criteria: Correlation coefficient |
Output model | PDB-7ata: |