Nudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): small class from symmetry expansion

2026-03-18 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update STRUCTURE_SUMMARY citation citation_author em_admin pdbx_entry_details _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2022-07-04 2022-12-28 2022-12-28 2026-03-18 Biotechnology and Biological Sciences Research Council (BBSRC) BB/L014130/1 United Kingdom Biotechnology and Biological Sciences Research Council (BBSRC) BBS/E/J/000PR9794 United Kingdom Wellcome Trust 108466/Z/15/Z United Kingdom Nudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): small class from symmetry expansion Castells-Graells R Hesketh EL Johnson JE Ranson NA Lawson DM Lomonossoff GP ICOSAHEDRAL VIRUS, AUTO-CATALYTIC CLEAVAGE, VIRUS MATURATION, VIRUS-LIKE PARTICLE, VIRUS LIKE PARTICLE Castells-Graells R Hesketh EL Matsui T Johnson JE Ranson NA Lawson DM Lomonossoff GP Unraveling the maturation pathway of a eukaryotic virus through cryo-EM. Proc.Natl.Acad.Sci.USA US 123 e2420493123 e2420493123 2026 41739563 doi:10.1073/pnas.2420493123 1091-6490 0040 PNASA6 8aay FULLOVERLAP EMDB EMD-15307 associated EM volume

Nudaurelia capensis omega virus Nudaurelia capensis omega virus 0 1

expressed in Spodoptera frugiperda Sf21 cells

Nudaurelia capensis omega virus Gonimbrasia cytherea 16.76 coat 415.0 4 VIRUS-LIKE PARTICLE OTHER false false p70 Nudaurelia capensis omega virus 0.06989195299999999 4 Spodoptera frugiperda LEVO MDSNSASGKRRSRNVRIAANTVNVAPKQRQARGRRARSRANNIDNVTAAAQELGQSLDANVITFPTNVATMPEFRSWARG KLDIDQDSIGWYFKYLDPAGATESARAVGEYSKIPDGLVKFSVDAEIREIYNEECPTVSDASIPLDGAQWSLSIISYPMF RTAYFAVANVDNKEISLDVTNDLIVWLNNLASWRDVVDSGQWFTFSDDPTWFVRIRVLHPTYDLPDPTEGLLRTVSDYRL TYKSITCEANMPTLVDQGFWIGGHYALTPIATTQNAVEGSGFVHPFNVTRPGIAAGVTLTWASMPPGGSAPSGDPAWIPD STTQFQWRHGGFDAPTGVITYTIPRGYTMQYFDTTTNEWNGFANPDDVVTFGQTGGAAGTNATITITAPTVTLTILATTT SAANVINFRNLDAETTAASNRSEVPLPPLTFGQTAPNNPKIEQTLVKDTLGSYLVHSKMRNPVFQLTPASSFGAISFTNP GFDRNLDLPGFGGIRDSLDVNMSTAVCHFRSLSKSCSIVTKTYQGWEGVTNVNTPFGQFAHSGLLKNDEILCLADDLATR LTGVYGATDNFAAAVLAFAANMLTSVLKSEATTSVIKELGNQATGLANQGLARLPGLLASIPGKIAARVRARRDRRRAAR MNNN Q4TVS9 singleParticle particle 0.3 5.6 COPPER 400 ETHANE FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.8 2.5 75000.0 NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 2 16478 1.0 49.1

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.

1 Gctf 1.06 PHASE FLIPPING AND AMPLITUDE CORRECTION 7ANM C1 3.39 FSC 0.143 CUT-OFF RELION 3.0.3

Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. The particles for this class were randomly split into half sets for the subsequent reconstruction and postprocessing steps. Note that the symmetry expansion step generates a 60-fold larger particle stack.

353898 MAXIMUM LIKELIHOOD RELION 3.0.3 MAXIMUM LIKELIHOOD RELION 3.0.3 RELION 3.0.3 emd_15307.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 766.80194 766.80194 766.80194 90.0 90.0 90.0 X Y Z -0.11339517 0.21590076 -0.00043386282 0.00838166 1.49766 1.49766 1.49766 0.025 AUTHOR ::::EMDATABANK.org::::EMD-15307:::: Postprocessed map from Relion 7ANM PDB experimental model OTHER Correlation coefficient REAL 78.0 emd_15307_msk_1.map emd_15307_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 766.80194 766.80194 766.80194 90.0 90.0 90.0 X Y Z -0.047081325 0.10485804 -0.00043406326 0.005932985 1.49766 1.49766 1.49766 AUTHOR ::::EMDATABANK.org::::EMD-15307:::: Refine3D half map 1 from Relion emd_15307_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 766.80194 766.80194 766.80194 90.0 90.0 90.0 X Y Z -0.04514629 0.10151253 -0.00043366238 0.0059410227 1.49766 1.49766 1.49766 AUTHOR ::::EMDATABANK.org::::EMD-15307:::: Refine3D half map 2 from Relion