2021-06-09 REL RCSB RCSB RCSB 2020-12-17 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 microscopy reconstruction of locally refined antibody DH898.1 Fab-dimer 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 2692-8205 EMD-23124 other EM volume EMD-23145 associated EM volume 7l6m FULLOVERLAP Antibody DH898.1 Fab-dimer bound to HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer Antibody DH898.1 Fab-dimer bound to HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer 0 1 2 3 0.0942 Antibody DH898.1 Fab-dimer 1 1 2 Macaca mulatta Homo sapiens 293F HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer 1 3 Human immunodeficiency virus 1 Homo sapiens singleParticle particle 1.5 7.5 5.0 HEPES buffer 150.0 NaCl sodium chloride Quantifoil R1.2/1.3 CARBON HOLEY ARRAY 12.0 GLOW DISCHARGE ETHANE 95 295 LEICA EM GP
2.5 microliters of sample applied to grid and incubated for 30 seconds in chamber, blotted for 2.5 seconds, and plunge frozen in liquid ethane.
For the DH898.1-bound complex, purified HIV-1 Env was mixed with 6-fold molar excess of recombinantly expressed and purified DH898.1 Fab to obtain a final Env concentration of 1.5 mg/ml, and incubated for 2 hours at room temperature.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.5 22500.0 GATAN K3 (6k x 4k) 3230 4.0 60.0 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
 CTFFIND 4.1.10 ab initio model generated directly from data. 1 C1 BACK PROJECTION 4.8 FSC 0.143 CUT-OFF cryoSPARC 2.15.0
Local refinement of Fab-dimer bound to SOSIP trimer, after particle subtraction to remove density for SOSIP trimer, and centered on Fab-dimer.
59012 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 2 31625.0 cryoSPARC 2.15.0 emd_23145.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 -0.63691163 0.8558629 0.00023892979 0.019697377 1.066496 1.066496 1.066496 0.25 AUTHOR Final density modified, masked, locally refined map of DH898.1 Fab dimer emd_23145_msk_1.map emd_23145_msk_2.map emd_23145_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 0.0 11.6087675 0.10567236 0.82924986 1.066496 1.066496 1.066496 AUTHOR Local resolution of locally refined map of DH898.1 Fab dimer emd_23145_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 -0.113664396 1.1327945 0.011643585 0.067093536 1.066496 1.066496 1.066496 AUTHOR Unmodified locally refined map of DH898.1 Fab dimer emd_23145_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 -0.7008892 1.2726061 0.006275445 0.111278266 1.066496 1.066496 1.066496 AUTHOR Half-map B of locally refined map of DH898.1 Fab dimer emd_23145_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 -0.76667464 1.3345518 0.006408867 0.11131317 1.066496 1.066496 1.066496 AUTHOR Half-map A of locally refined map of DH898.1 Fab dimer