2024-05-15 REL PDBe PDBe PDBe 2017-09-12 2017-10-18 2018-07-18 2024-05-15 European Research Council FP/2007-2013 (355855) Czech Republic European Molecular Biology Organization IG-3041 Czech Republic Sacbrood virus of honeybee - expansion state II Plevka P Prochazkova M empty particle, icosahedral virus particle, iflavirus, expanded particle, VIRUS Prochazkova M Fuzik T Skubnik K Moravcova J Ubiparip Z Pridal A Plevka P Virion structure and genome delivery mechanism of sacbrood honeybee virus. Proc. Natl. Acad. Sci. U.S.A. US 115 7759 7764 2018 29987012 doi:10.1073/pnas.1722018115 1091-6490 0040 PNASA6 6eh1 FULLOVERLAP Sacbrood virus Sacbrood virus 0 1 2 3 4
Isolated from honeybee pupae
Sacbrood virus Apis mellifera capsid 278.86 3 VIRION STRAIN false true structural protein VP1 Sacbrood virus 0.02427948 1 LEVO IKDILRRPVLLFNHVELDPDYTGFFIPIMPPSRMMQYKSGDKETSFQRLIGRTPQAAIMNLFRFWRGSLRYTIIIHSTDG HPIYVTHVPHTGNRVYGLMKVNNLHEYTKVPIFGCGLTTEMIIPSVNPSICVEVPFDTENNWAVTFDEDAQRNYSWRDKG DTVTGHLVVTPVVSVYMSVWVEAGDDFEVSNFYGPPSVKTNDWNYAFSDEH A0A223FUL8 structural protein VP2 Sacbrood virus 0.020360313999999997 1 LEVO WMPINSIRVTVNGKRNDLLAQYYIPEDFLSTHAKCAPNTIPFETYVYGKYELEMKFVANGNKFQCGKVIISVKFDSYQAD NINTGFQAALSRPHIMLDLSTNNEGVLKIPFRYHRAFVRNQTHKTATAGVRPGKFASIYVQVLSPLQTGEGGANDMFIRP FYRYTRAEFAGMSYKVPLT A0A223DN66 structural protein VP3 Sacbrood virus 0.025574461 1 LEVO DEPRTTLDIARIWGLRSTFNWGSGDEHGKELFNTVLDPGLRFYDQDYEGQITPMEYVTGLYNFWSGPIELRFDFVSNAFH TGTVIISAEYNRSSTNTDECQSHSTYTKTFHLGEQKSVHFTVPYIYDTVVRRNTASAYLPVTDYDKVDNVSRAQAMGIRA ESKMRVKVRVVNVLRPVASTTSTIEVLVYMRGGKNYALHGLKQSTYWPSNSVVPIDSFPPDGYDP A0A223DN66 minor capsid protein MiCP Sacbrood virus 0.003107398 1 LEVO DNPHRFLPANVSNRWNEYSSAYLPRV Q9IGK7 singleParticle particle 15 5.8 137.0 NaCl sodium chloride 2.7 KCl potassium chloride 10.0 Na2HPO4 disodium phosphate 1.8 KH2PO4 potassium phosphate Quantifoil R2/1 COPPER 300 GLOW DISCHARGE OTHER 101.325 ETHANE 70 298 FEI VITROBOT MARK II FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 4.0 75000.0 74325.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
Preliminar grid screening was performed manually on FEI Tecnai F20 (cryo stage).
FEI FALCON II (4k x 4k) COUNTING 4096 4096 2-16 1 1.0 21.0 1 51000
Full virions were selected together with empty particles from the same set of micrographs. Subsequent 2D classification sorted the particles of two types. Full and empty particles were further processed separately. Full particles classified in two types - expansion state I and II.
 5CDC
Deposited IAPV model low pass filtered to resolution 40 A.
 1 FOURIER SPACE 7.25 FSC 0.143 CUT-OFF RELION 2 5330 OTHER PROJECTION MATCHING RELION 2 relion_refine_mpi 3 RELION 2
re-classification after initial 3D refinement
 emd_3867.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 546 546 546 -273 -273 -273 546 546 546 580.398 580.398 580.398 90.0 90.0 90.0 X Y Z -0.12586766 0.21891223 0.0012369186 0.010741303 1.063 1.063 1.063 4.5 EMDB RIGID BODY FIT R-factor REAL 268.70999999999998