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- EMDB-15266: Nudaurelia capensis omega virus maturation intermediates captured... -
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Open data
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Basic information
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Title | Nudaurelia capensis omega virus maturation intermediates captured at pH5.6 (insect cell expressed VLPs): consensus map | ||||||||||||
![]() | Postprocessed map from Relion | ||||||||||||
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Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||||||||
![]() | Castells-Graells R / Hesketh EL / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Decoding virus maturation with cryo-EM structures of intermediates Authors: Castells-Graells R / Hesketh EL / Johnson JE / Ranson NA / Lawson DM / Lomonossoff GP | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 465.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17 KB 17 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18 KB | Display | ![]() |
Images | ![]() | 223.5 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() | 408.7 MB 408.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 787.2 KB | Display | ![]() |
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Full document | ![]() | 786.7 KB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Postprocessed map from Relion | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.49766 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Refine3D half map 2 from Relion
File | emd_15266_half_map_1.map | ||||||||||||
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Annotation | Refine3D half map 2 from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half map 1 from Relion
File | emd_15266_half_map_2.map | ||||||||||||
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Annotation | Refine3D half map 1 from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Nudaurelia capensis omega virus
Entire | Name: ![]() ![]() |
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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: all / Details: expressed in Spodoptera frugiperda Sf21 cells / 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: ![]() |
Molecular weight | Theoretical: 16.76 MDa |
Virus shell | Shell ID: 1 / Name: coat / Diameter: 430.0 Å / T number (triangulation number): 4 |
-Macromolecule #1: Nudaurelia capensis omega virus coat protein
Macromolecule | Name: Nudaurelia capensis omega virus coat protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
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 VYGATDNFAA AVLAFAANML TSVLKSEATT SVIKELGNQA TGLANQGLAR LPGLLASIPG KIAARVRARR DRRRAAR MN NN |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 5.6 |
Grid | Material: COPPER / Mesh: 400 |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 16478 / Average exposure time: 1.0 sec. / Average electron dose: 49.1 e/Å2 Details: Reconstructed from 2 datasets collected at doses of 48.7 and 50.4 electrons per Angstrom squared, respectively. The average of these two values is given. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Details | No model was generated from the consensus map |
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