2021-09-08 REL RCSB RCSB RCSB 2020-12-31 2021-08-04 2021-08-04 2021-09-08 International AIDS Vaccine Initiative OPP1196345 United States Antanasijevic A Sewall LM Ward AB Antanasijevic A Sewall LM Cottrell CA Carnathan DG Jimenez LE Ngo JT Silverman JB Groschel B Georgeson E Bhiman J Bastidas R LaBranche C Allen JD Copps J Perrett HR Rantalainen K Cannac F Yang YR de la Pena AT Rocha RF Berndsen ZT Baker D King NP Sanders RW Moore JP Crotty S Crispin M Montefiori DC Burton DR Schief WR Silvestri G Ward AB Nat Commun UK 12 4817 4817 2021 34376662 doi:10.1038/s41467-021-25087-4 2041-1723 EMD-23231 other EM volume EMD-23232 other EM volume EMD-23233 other EM volume EMD-23180 other EM volume EMD-23234 associated EM volume BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-5 from animal Rh.33172 (Wk38 time point) BG505 SOSIP.v5.2(7S) in complex with the polyclonal Fab pAbC-5 from animal Rh.33172 (Wk38 time point) 0 1

Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification. Map and model were reconstructed from the immune complex dataset using the focused classification approach.

Human immunodeficiency virus 1 Homo sapiens Envelope glycoprotein gp160 Human immunodeficiency virus 1 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTVKSIRIGPGQWFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLELD singleParticle particle 6 7.4 20.0 Tris-HCl Tris-HCl 150.0 NaCl Sodium chloride

TBS buffer prepared from a 10X stock

UltrAuFoil R1.2/1.3 GOLD 300 CARBON HOLEY PLASMA CLEANING OTHER ETHANE 100 283 FEI VITROBOT MARK IV

Blotting time varied between 3 and 7 seconds..

Polyclonal complexes were generated by incubation of isolated polyclonal Fabs with recombinantly expressed BG505 SOSIP and subsequent SEC purification.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.6 1.6 29000.0 OTHER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-36 4 4521 9.0 50.7 1

Frames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.

1121581

Particles picked using template picker

RELION 3.0

3D map of the free HIV Env trimer ectodomain, low-pass filtered to 20A

1 C1 BACK PROJECTION 4.5 FSC 0.143 CUT-OFF RELION 3.0

33802 symmetry expanded particles. See the Methods section in the manuscript for details.

33802 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0

Multi-step focused classification was applied to isolate the particles featuring this type fo polyclonal antibody. See the Method section of the manuscript for details

6VL5 4KTE RIGID BODY FIT REAL emd_23234_msk_1.map emd_23234_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 329.59998 329.59998 329.59998 90.0 90.0 90.0 X Y Z -0.029631454 0.05906397 0.00018252779 0.0029333136 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-23234:::: 3D map of BG505 SOSIP v5.2(7S) in complex with the polyclonal Fab pAbC-5 from animal Rh.33172 (Wk38 time point). Half-map 1 emd_23234_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 329.59998 329.59998 329.59998 90.0 90.0 90.0 X Y Z -0.02881615 0.062224697 0.00014013685 0.0028975501 1.03 1.03 1.03 AUTHOR ::::EMDATABANK.org::::EMD-23234:::: 3D map of BG505 SOSIP v5.2(7S) in complex with the polyclonal Fab pAbC-5 from animal Rh.33172 (Wk38 time point). Half-map 2