2024-07-17 REL PDBe PDBe PDBe 2023-07-17 2024-07-17 2024-07-17 2024-07-17 Grant Agency of the Czech Republic GX19-25982X Czech Republic Ministry of Education, Youth and Sports of the Czech Republic LX22NPO5103 Czech Republic Tick-borne encephalitis virus (strain HYPR) immature particle Fuzik T Plevka P Smerdova L Novacek J immature particle, tick-borne, flavivirus, whole particle, VIRUS Anastasina M Fuzik T Domanska A Pulkkinen LIA Smerdova L Formanova PP Strakova P Novacek J Ruzek D Plevka P Butcher SJ The structure of immature tick-borne encephalitis virus supports the collapse model of flavivirus maturation. Sci Adv US 10 eadl1888 eadl1888 2024 38959313 doi:10.1126/sciadv.adl1888 2375-2548 Tick-borne encephalitis virus Tick-borne encephalitis virus 0 1 2
Immature particles produced using tissue cell cultures
Tick-borne encephalitis virus HYPR immature particle 600.0 VIRION STRAIN true false Envelope protein E Tick-borne encephalitis virus HYPR LEVO SRCTHLENRDFVTGTQGTTRVTLVLELGGCVTITAEGKPSMDVWLDAIYQENPAQTREYCLHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDRGWGNHCGLFGKGSIVACVKAACEAKKKATGHVYDANKIVYTVKVEPHTGDYVAANETHSGRKTASFTVSSEKTILTMGEYGDVSLLCRVASGVDLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGARNWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTKYHLKSGHVTCEVGLEKLKMKGLTYTMCDKTKFTWKRAPTDSGHDTVVMEVTFSGTKPCRIPVRAVAHGSPDVNVAMLITPNPTIENNGGGFIEMQLPPGDNIIYVGELSYQWFQKGSSIGRVFQKTKKGIERLTVIGEHAWDFGSAGGFLSSIGKALHTVLGGAFNSIFGGVGFLPKLLLGVALAWLGLNMRNPTMSMSFLLAGVLVLAMTLGVGA Q01299 Protein prM Tick-borne encephalitis virus HYPR LEVO TVRKERDGSTVIRAEGKDAATQVRVENGTCVILATDMGSWCDDSLSYECVTIDQGEEPVDVDCFCRNVDGVYLEYGRCGKQEGSRTRRSVLIPSHAQGELTGRGHKWLEGDSLRTHLTRVEGWVWKNRLLALAMVTVVWLTLESVVTRVAVLVVLLCLAPVYA Q01299 singleParticle particle 2 8.5 20.0 Tris Trizma 120.0 NaCl Sodium Chloride 1.0 EDTA Quantifoil R2/1 COPPER 300 CARBON HOLEY 2.0 GLOW DISCHARGE OTHER ETHANE 100 280 FEI VITROBOT MARK IV
purified immature particles of Tick-borne encephalitis virus
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 1.0 3.0 75000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON III (4k x 4k) INTEGRATING 1 2262 1.0 69.0
collected in movie mode total 39 fractions per micrograph
 1 29978
autopicking performed by manually trained crYOLO neural network
 SGD ab initio model
RELION v 3.1
 1 I FOURIER SPACE 8.64 FSC 0.143 CUT-OFF RELION 3.1 18160 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 emd_17945.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 829.44 829.44 829.44 90.0 90.0 90.0 X Y Z -0.071375586 0.117002144 0.0012894522 0.007623622 1.62 1.62 1.62 0.025 AUTHOR immature particle of tick-borne encephalitis virus (strain HYPR) emd_17945_msk_1.map emd_17945_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 829.44 829.44 829.44 90.0 90.0 90.0 X Y Z -0.016295074 0.046087686 0.0008017576 0.005836353 1.62 1.62 1.62 AUTHOR half map 2 of Gold-standard reconstruction of immature particle of tick-borne encephalitis virus (strain HYPR) emd_17945_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 -256 -256 -256 512 512 512 829.44 829.44 829.44 90.0 90.0 90.0 X Y Z -0.01770022 0.046653982 0.00080161105 0.005836243 1.62 1.62 1.62 AUTHOR half map 1 of Gold-standard reconstruction of immature particle of tick-borne encephalitis virus (strain HYPR)