2021-04-28 REL PDBe PDBe PDBe 2018-07-31 2018-08-08 2018-08-08 2021-04-28 Medical Research Council (United Kingdom) MC_UP_A025_1013 United Kingdom RELION-3.0 reconstruction of influenza hemagglutinin (HA) trimer using particles from micrographs tilted at 40 degrees in EMPIAR-10097 Zivanov J Nakane T Scheres SHW Zivanov J Nakane T Forsberg BO Kimanius D Hagen WJ Lindahl E Scheres SH New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife US 7 2018 30412051 doi:10.7554/eLife.42166 2050-084X Tan YZ Baldwin PR Davis JH Williamson JR Potter CS Carragher B Lyumkis D Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat. Methods US 14 793 796 2017 28671674 doi:10.1038/nmeth.4347 1548-7105 EMD-8731 other EM volume
EMDB 8731 and EMPIAR-10097 are from the original authors. Our deposition is re-processing of raw data with RELION 3.0.
 EMD-0152 associated EM volume Influenza hemagglutinin (HA) trimer Influenza hemagglutinin (HA) trimer 0 1 2 Homo sapiens 0.15 Influenza hemagglutinin HA1 chain A/Hong Kong/1/1968 H3N2 Homo sapiens HEK293 LEVO ADPGATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDL FVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNV TMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVIN SNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEK QTR Influenza hemagglutinin HA2 chain A/Hong Kong/1/1968 H3N2 Homo sapiens HEK293 LEVO GLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDL EKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTGRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHD VYRDEALNNRFQIK singleParticle particle 0.75 7.4
PBS Buffer
 ETHANE 80 GATAN CRYOPLUNGE 3
3 microliters of 0.75 mg/mL sample was added to a plasma-cleaned (Gatan Solarus) 1.2-micron-hole, 1.3-micron-spacing holey gold grid (made in-house) and plunge-frozen in liquid ethane using the Cryoplunge 3 system (Gatan) operating at 80% humidity, 298K ambient temperature..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 1.0 3.5 22500.0 38167.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
In order to account for highly preferred orientations of the specimen, data were acquired using tilts of 40 degrees.
GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 1-100 82.0 1 608919 CTFFIND 4.1.10 For initial estimation RELION 3.0 CTF refinement
Standard CTF correction inside RELION's reconstruction.
 1 C3 FOURIER SPACE 3.1 FSC 0.143 CUT-OFF RELION 3.0 151596 MAXIMUM LIKELIHOOD RELION 3.0
RELION SGD
 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_0152.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 282.96 282.96 282.96 90.0 90.0 90.0 X Y Z -0.30286443 0.39587775 5.9126514e-06 0.0112498915 1.31 1.31 1.31 0.078 AUTHOR postprocessed map emd_0152_msk_1.map emd_0152_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 282.96 282.96 282.96 90.0 90.0 90.0 X Y Z -0.047949675 0.099323906 5.923738e-06 0.0034396811 1.31 1.31 1.31 AUTHOR unfiltered half map 2 emd_0152_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 216 216 216 0 0 0 216 216 216 282.96 282.96 282.96 90.0 90.0 90.0 X Y Z -0.036682755 0.1016331 5.901568e-06 0.0034351146 1.31 1.31 1.31 AUTHOR unfiltered half map 1