Cryo-electron microscopy local refinement of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer

2021-06-09 REL RCSB RCSB RCSB 2020-12-17 2021-03-03 2021-03-03 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 local refinement of antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848 10.17 SOSIP trimer 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 other EM volume EMD-23149 other EM volume EMD-23152 other EM volume EMD-23153 associated EM volume Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer Antibody DH898.1 Fab-dimer bound to glycans 332, 392, and 396 of HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer 0 1 2 3 0.304 HIV Env CH848.3.D0949.10.17chim.6R.DS.SOSIP.664 trimer 1 3 Human immunodeficiency virus 1 Homo sapiens 293F 0.210 Antibody DH898.1 Fragment antigen binding (Fab) dimer 1 1 2

Composed of two heavy chains and two light chains

Macaca mulatta Homo sapiens 293F 0.094 DH898.1 Fab heavy chain Macaca mulatta LEVO QDLLLQSGAEVREPGASVTVSCQASNYTFPDYYIHWVRLVPGQGLEWLGEMKPKVGVTNVSKKIRDRLFMTADTSTDTAYMVLSALTPGDTAIYYCTRLEPDFLSGWAHWGKGVLVTVSPASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPVTVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVE DH898.1 Fab light chain Macaca mulatta LEVO EIVMTQTPLSLSVTPGEPASLSCRSSASLLHGNGNTYLHWYLRKAGQSPQLLIFGGSKRVPGISDRFIGSGAGTNFTLKISSVEADDVGFYYCAQGVAFPWTFGQGTKVEIKRAVAAPSVFIFPPSEDQVKSGTVSVVCLLNNFYPREASVKWKVDGVLKTGNSQESVTEQDSKDNTYSLSSTLTLSNTDYQSHNVYACEVTHQGLSSPVTKSFNRGE 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 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 generated directly from data. 1 C1 BACK PROJECTION 7.0 FSC 0.143 CUT-OFF cryoSPARC 2.15.0 14873 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 MAXIMUM LIKELIHOOD cryoSPARC 2.15.0 4 10132.0 cryoSPARC 2.15.0

Ab initio

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