2021-06-09 REL RCSB RCSB RCSB 2020-12-16 2021-02-10 2021-02-10 2021-06-09 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI140897 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI145687 United States Cryo-electron microcospy reconstruction of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env Edwards RJ Acharya P Williams WB Meyerhoff RR Edwards RJ Li H Manne K Nicely NI Henderson R Zhou Y Janowska K Mansouri K Gobeil S Evangelous T Hora B Berry M Abuahmad AY Sprenz J Deyton M Stalls V Kopp M Hsu AL Borgnia MJ Stewart-Jones GBE Lee MS Bronkema N Moody MA Wiehe K Bradley T Alam SM Parks RJ Foulger A Oguin T Sempowski GD Bonsignori M LaBranche CC Montefiori DC Seaman M Santra S Perfect J Francica JR Lynn GM Aussedat B Walkowicz WE Laga R Kelsoe G Saunders KO Fera D Kwong PD Seder RA Bartesaghi A Shaw GM Acharya P Haynes BF Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 184 2955 2972.e25 2021 34019795 doi:10.1016/j.cell.2021.04.042 1097-4172 Williams WB Meyerhoff RR Edwards RJ Li H Nicely NI Henderson R Zhou Y Janowska K Mansouri K Manne K Stalls V Hsu AL Borgnia MJ Stewart-Jones G Lee MS Bronkema N Perfect J Moody MA Wiehe K Bradley T Kepler TB Alam SM Foulger A Bonsignori M LaBranche CC Montefiori DC Seaman M Santra S Francica JR Lynn GM Aussedat B Walkowicz WE Laga R Kelso G Saunders KO Fera D Kwong PD Seder RA Bartesaghi A Shaw GM Acharya P Haynes BF Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques bioRxiv US https://doi.org/10.1101/2020.06.30.178921 2020 doi:10.1101/2020.06.30.178921 EMD-23124 associated EM volume 7l6o FULLOVERLAP HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 unliganded trimer in the presence of but not bound to DH898.1 Fab 0 1 2 Human immunodeficiency virus 1 CH848 10.17 Homo sapiens 293F 0.2097 CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp120 Human immunodeficiency virus 1 Homo sapiens LEVO AENLWVTVYYGVPVWKEAKTTLFCASDARAYEKEVHNVWATHACVPTDPSPQELVLGNVTENFNMWKNDMVDQMHEDIIS LWDQSLKPCVKLTPLCVTLICSNATVKNGTVEEMKNCSFNTTTEIRDKEKKEYALFYKPDIVPLSETNNTSEYRLINCNT SACTQACPKVTFEPIPIHYCAPAGYAILKCNDETFNGTGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEKEIVIRSENLT NNAKIIIVHLHTPVEIVCTRPNNNTRKSVRIGPGQTFYATGDIIGDIKQAHCNISEEKWNDTLQKVGIELQKHFPNKTIK YNQSAGGDMEITTHSFNCGGEFFYCNTSNLFNGTYNGTYISTNSSANSTSTITLQCRIKQIINMWQGVGRCMYAPPIAGN ITCRSNITGLLLTRDGGTNSNETETFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGR CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 - gp41 Human immunodeficiency virus 1 LEVO FLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGC SGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD singleParticle particle 1.5 7.5 5.0 HEPES buffer 150.0 NaCl sodium chloride C-flat-1.2/1.3 COPPER 300 CARBON HOLEY 12.0 GLOW DISCHARGE 0.039
Glow discharged for 30 s in PELCO easiGlow(TM).
 ETHANE 95 293 LEICA EM GP
2.5 microliter of smaple applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.5 22500.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 93.15 93.15 GATAN K3 (6k x 4k) 3230 4.0 62.0 1 1655400
Particles were picked using Blob Picker on 500 micrographs with a minimum and maximum particle diameter of 150 and 250 angstroms for circular blobs, yielding 259,587 particles, which were extracted with a 320-pixel box size and subjected to 2D class averaging with 100 classes. From these, seven classes were chosen for template picking applied to the full final micrograph set, yielding 1,655,400 particles
 cryoSPARC 6UM6 1 C3 BACK PROJECTION 3.9 FSC 0.143 CUT-OFF cryoSPARC 2.15.0 48127 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 4 17329.0 cryoSPARC 2.15.0
Ab initio
 emd_23124.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.02298 273.02298 273.02298 90.0 90.0 90.0 X Y Z -0.5204865 1.6141689 0.0125683425 0.06454605 1.066496 1.066496 1.066496 0.45 AUTHOR Final sharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env 6UM6 AB INITIO MODEL emd_23124_msk_1.map emd_23124_msk_2.map emd_23124_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.02298 273.02298 273.02298 90.0 90.0 90.0 X Y Z -0.06522821 0.7040421 0.013571677 0.059032533 1.066496 1.066496 1.066496 AUTHOR Unsharpened map of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env emd_23124_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.02298 273.02298 273.02298 90.0 90.0 90.0 X Y Z 0.0 10.624056 0.5097363 1.7976962 1.066496 1.066496 1.066496 AUTHOR Local resolution of of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env emd_23124_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.02298 273.02298 273.02298 90.0 90.0 90.0 X Y Z -0.24909212 0.76256937 0.0074867913 0.06596262 1.066496 1.066496 1.066496 AUTHOR Half-map B of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env emd_23124_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 273.02298 273.02298 273.02298 90.0 90.0 90.0 X Y Z -0.25403035 0.7844281 0.0075632115 0.066047 1.066496 1.066496 1.066496 AUTHOR Half-map A of CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 HIV Env