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- EMDB-15307: Nudaurelia capensis omega virus maturation intermediate captured ... -
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Open data
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Basic information
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Title | Nudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): small class from symmetry expansion | ||||||||||||
![]() | Postprocessed map from Relion | ||||||||||||
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![]() | ICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / VIRUS-LIKE PARTICLE / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Peptidase N2 / Peptidase family A21 / Viral coat protein subunit / p70![]() | ||||||||||||
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 | ![]() | 468.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.5 KB 18.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18 KB | Display | ![]() |
Images | ![]() | 223.5 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 410.8 MB 410.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aayMC ![]() 8a6jC ![]() 8ac6C ![]() 8achC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Postprocessed map from Relion | ||||||||||||||||||||
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 1 from Relion
File | emd_15307_half_map_1.map | ||||||||||||
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Annotation | Refine3D half map 1 from Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Refine3D half map 2 from Relion
File | emd_15307_half_map_2.map | ||||||||||||
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Annotation | Refine3D half map 2 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: 415.0 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: ![]() ![]() |
Molecular weight | Theoretical: 69.891953 KDa |
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 UniProtKB: p70 |
-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
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: OTHER / Overall B value: 78 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-8aay: |