Single particle reconstruction of slow bee paralysis virus virion at pH 5.5

2024-05-15 REL PDBe PDBe PDBe 2016-07-21 2016-10-19 2017-02-15 2024-05-15 Single particle reconstruction of slow bee paralysis virus virion at pH 5.5 Kalynych S Fuzik T Plevka P icosahedral virus, honebee virus, iflavirus, virus Kalynych S Fuzik T Pridal A de Miranda J Plevka P Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism. Proc. Natl. Acad. Sci. U.S.A. US 114 598 603 2017 28053231 doi:10.1073/pnas.1616562114 1091-6490 0040 PNASA6 5lk7 FULLOVERLAP Slow bee paralysis virus Slow bee paralysis virus 0 1 2 3 Slow bee paralysis virus Apis mellifera 3 icosahedral VIRION SPECIES false false VP1 Slow bee paralysis virus 0.030307210999999997 1 LEVO MERTFTPNVMQPTPLLPTTNDGRVTFGEAFNDLKDLARRYQLYWEGTILEGNLRAIRRNSALVQLPLYPHGLRIQPDVNN PIWNIMRDGHIPVISSGFRYFRGGLRLRIVVEGLNSCVWVQHHPDRPSIFSRPIIGRYIAAKDAYRNHAYAAYVQNMSVN RTIEVEVPFYQPGLYGMLNASDNNTANSFDRLRFTGLGDLLIGIEGEQPIPKEGIEISVYYSIADDFSFNIFCGFPPMVY CDETYSAATPDLAQYFEDEVTIAQPE A7LM73 VP2 Slow bee paralysis virus 0.029824205 1 LEVO MDRPEGSEERTVQTSNVVLGETNIESQDIASKEYSPTWDRLASSEVSDEYPMLTDRWLFWKSVKWEVNDSAFGKMLVQEK FPQSWVQMDVNVNNIPRYTNIPNFIPFNIHQYMRADFEVKIYVNPNDFVSGWLIMAFLYQGSEMFDYKLRRNPAALMQMP HVLVNVGAANEATLKIPYRYVRPFMRCKDILRGDNLITGVTEPLNMGVLFVEVLIPFRTSAASSAPKSLDVSLFVKMTNA KFTGMVDGSIALLSKPIALPE A7LM73 VP3 Slow bee paralysis virus 0.04762391 1 LEVO DNPPDPTPAKFFVPIPSHSWAHGTNTSEPTNTLRLDGGVVGVGRSDDIGTSDTAISGIIGVYGLLKPFDWNANDTGRNVG GHLLWSMPVHPQVDKDQVIQVMTQSKLTQYYLPPISVVSSLYAYTRGSIKYKFLFGNNPRHNARLLVAYIPGISSDNRLT LERARNSAHVVFSLNEVSEFVFTVPYITDTMWWPRKYGGPQAAGEFVAPSYICMFILNPLVAMESVPSIVTIVPMIAAGD DFEVAVPAQPAVGLSRNIDVIYPKDSIISFKSGYFPVYVGSWHSFFDSTKAILRYGAVSDHIAQLGNIPANVNRKAFWIV VGDTIKFKTKLDKINGTEWFIPEGEYTLGYGVVWRDGAYAYMVPYPLTPLGEKIAQYTASLLASNTAISQIRPYIPDYIV DSAASKDNILWSPIEDRLRAQTEWVMAEPE A7LM73 singleParticle particle 1.8 5.5

30 mM Sodium Acetate 50 mM Sodium Chloride

Quantifoil R2/1 COPPER 300 ETHANE FEI VITROBOT MARK IV

blot force 0, blot time 2 s..

sample was purifed froim natural source and dialyzed overnight into sodium acetate buffer

FEI TITAN KRIOS OTHER BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 3.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON II (4k x 4k) INTEGRATING 4096 4096 1-7 1 5325 0.5 21.0 1 4712 5J98

devoid of the protruding domains.

FOURIER SPACE 3.42 FSC 0.143 CUT-OFF RELION 1.4 10350 NOT APPLICABLE OTHER RELION 3.1

RELION 3D refinement was used for angle assignment & refinement

4 RELION 1.4

RELION 3D classification was used for final classification

emd_4063.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 380 380 380 -190 -190 -190 380 380 380 406.6 406.6 406.6 90.0 90.0 90.0 Y X Z -9.694521999999999 14.482196 -0.000000000696011 1.0000001 1.07 1.07 1.07 4.66 AUTHOR ::::EMDATABANK.org::::EMD-4063:::: single particle reconstruction of SBPV virion at low pH OTHER RECIPROCAL 49.700000000000003