2020-01-29 REL RCSB RCSB RCSB 2017-05-14 2017-06-14 2017-06-14 2020-01-29 Agency for Science, Technology and Research Singapore Singapore US National Institutes of Health (NIH) DP5 OD021396-01 United States Leona M. and Harry B. Helmsley Charitable Trust Grant 2017-PG-MED001 United States National Institute of Aging K99 transitional award AG050749 United States Jane Coffin Childs Foundation post-doctoral fellowship United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM053757 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) GM103310 United States Simons Foundation 349247 United States Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees Tan Y Baldwin PR Potter CS Carragher B Lyumkis D 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 associated EM volume Influenza hemagglutinin (HA) trimer Influenza hemagglutinin (HA) trimer 0 1
A/Hong Kong/1/1968 (H3N2), obtained commercially from MyBioSource, catalog MBS434205
Influenza A virus (A/Hong Kong/1/1968(H3N2)) 0.15 Homo sapiens HEK293 Influenza hemagglutinin (HA) Trimer A/Hong Kong/1/1968 H3N2 Influenza A virus (A/Hong Kong/1/1968(H3N2)) Homo sapiens LEVO QDLPGNDNSTATLCLGHHAVPNGTLVKTITDDQIEVTNATELVQSSSTGKICNNPHRILDGIDCTLIDALLGDPHCDVFQNETWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFITEGFTWTGVTQNGGSNACKRGPGSGFFSRLNWLTKSGSTYPVLNVTMPNNDNFDKLYIWGVHHPSTNQEQTSLYVQASGRVTVSTRRSQQTIIPNIGSRPWVRGLSSRISIYWTIVKPGDVLVINSNGNLIAPRGYFKMRTGKSSIMRSDAPIDTCISECITPNGSIPNDKPFQNVNKITYGACPKYVKQNTLKLATGMRNVPEKQTRGLFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTRRQLRENAEDMGNGCFKIYHKCDNACIESIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKD singleParticle particle 0.75 7.4 137.0 NaCl Sodium Chloride 2.7 KCl Potassium Chloride 10.0 Na2HPO4 Disodium Phosphate 1.8 KH2PO4 Monopotassium Phosphate
PBS Buffer
 C-Flat CF-1.2/1.3-4Au GOLD 400 HOLEY PLASMA CLEANING OTHER ETHANE 80 298 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..
Fraction was obtained directly from a sucrose gradient, and was spin-concentrated in a 100 kDa MW-cutoff filter.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 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. The CTF was estimated on a per-particle basis to account for the gradient of CTF values across individual micrographs.
GATAN K2 SUMMIT (4k x 4k) COUNTING 3710 3838 5.0 1-100 2 847 20.0 82.0 1 287820
287820 particles were picked using Gautomatch with templates made from an initial 2D classification of a subset of the particles. These particles were put through 2D classification to produce 158432 particles.
 Gctf 0.5 Ab initio model was produced using CryoSPARC using the 158432 particles. 1 C3 FOURIER SPACE 4.2 FSC 0.143 CUT-OFF RELION 2
Directional anisotropy is present in the resolution, with a range from 3.7 to 5.5 Angstrom, 3D FSC sphericity of 0.97, and map-to-model resolution of 4.4 Angstrom.
158432 PROJECTION MATCHING RELION 2 PROJECTION MATCHING RELION 2 emd_8731.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.071533866 0.13927907 -0.00001959061 0.004145391 1.31 1.31 1.31 0.0367 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, sharpened using a B-factor of 320 emd_8731_msk_1.map emd_8731_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.008629856 0.06308579 -0.00001949124 0.002482918 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, unsharpened emd_8731_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 143 143 143 -72 -72 -72 143 143 143 187.32999 187.32999 187.32999 90.0 90.0 90.0 X Y Z 0 1 0.045838326 0.17125797 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, map-to-model 3DFSC, thresholded at 0.5 emd_8731_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 143 143 143 -72 -72 -72 143 143 143 187.32999 187.32999 187.32999 90.0 90.0 90.0 X Y Z 0 1 0.08315212 0.2359162 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, half-map 3DFSC, thresholded at 0.143 emd_8731_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 143 143 143 -71 -71 -71 143 143 143 187.32999 187.32999 187.32999 90.0 90.0 90.0 X Y Z -0.17322367 1 0.07197801 0.19182976 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, map-to-model 3DFSC, raw emd_8731_additional_5.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 143 143 143 -71 -71 -71 143 143 143 187.32999 187.32999 187.32999 90.0 90.0 90.0 X Y Z -0.18454453 1 0.08620734 0.23714294 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, half-map 3DFSC, raw emd_8731_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.011862308 0.06730088 -0.00001842417 0.0025864898 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, half map 1 emd_8731_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.013026363 0.06625888 -0.00001812810 0.002584418 1.31 1.31 1.31 AUTHOR Influenza hemagglutinin (HA) trimer reconstruction at 4.2 Angstrom resolution using particles from micrographs tilted at 40 degrees, half map 2