2024-10-16 REL RCSB RCSB RCSB 2021-01-01 2021-08-04 2021-08-04 2024-10-16 International AIDS Vaccine Initiative OPP1196345 United States BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point) Antanasijevic A Sewall LM HIV, vaccine design, BG505, VIRAL PROTEIN, Polyclonal antibodies, EMPEM, VIRAL PROTEIN-Immune System complex 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 Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Nat Commun UK 12 4817 4817 2021 34376662 doi:10.1038/s41467-021-25087-4 2041-1723 EMD-23236 other EM volume EMD-23237 other EM volume EMD-23238 other EM volume EMD-23239 other EM volume EMD-23240 other EM volume EMD-23241 other EM volume EMD-23242 other EM volume EMD-23176 other EM volume 7l90 FULLOVERLAP BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point) BG505 SOSIP.v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point) 0 1 2 3 4
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.
 BG505 SOSIP.v5.2 N241/N289 gp120/gp41 1 1 2 Human immunodeficiency virus 1 polyclonal Fab pAbC-8 from animal Rh.33311 1 3 4 Macaca mulatta BG505 SOSIP.v5.2 N241/N289 - gp120 Human immunodeficiency virus 1 0.056417125 3 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTD PNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELR DKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGP CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTRKSIRIGPGQWFYAT GDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNT SVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWR SELYKYKVVKIEPLGVAPTRCKR BG505 SOSIP.v5.2 N241/N289 - gp41 Human immunodeficiency virus 1 0.016477719000000002 3 Homo sapiens LEVO LGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKLTVWGIKQLQARVLAVERYLRDQQLLGIWGCS GKLICCTNVPWNSTWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD Rh.33311 pAbC-8 - Heavy Chain Macaca mulatta 0.009209344
This is a polyclonal antibody and the sequence is inherently unknown. Poly-alanine pseudo-model is used to depict the backbone of this antibody.
1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) Rh.33311 pAbC-8 - Light Chain Macaca mulatta 0.00793277
This is a polyclonal antibody and the sequence is inherently unknown. Poly-alanine pseudo-model is used to depict the backbone of this antibody.
1 LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 52 NAG 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 1-39 4 6268 9.75 44.3 1
Frames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
1267693
Particles picked using template picker
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
29622 symmetry-expanded particles. See the Methods section of the manuscript for details.
29622 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
 emd_23243.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 370.8 370.8 370.8 90.0 90.0 90.0 X Y Z -0.031038472 0.057612676 0.00015816854 0.002190224 1.03 1.03 1.03 0.017 AUTHOR 3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point). Main map 6VL5 PDB experimental model 4KTE PDB experimental model RIGID BODY FIT REAL emd_23243_msk_1.map emd_23243_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 370.8 370.8 370.8 90.0 90.0 90.0 X Y Z -0.02454711 0.049938716 0.00015415828 0.0029279606 1.03 1.03 1.03 AUTHOR 3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point). Half-map 1 emd_23243_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 370.8 370.8 370.8 90.0 90.0 90.0 X Y Z -0.023016373 0.04613567 0.0001621788 0.0028935722 1.03 1.03 1.03 AUTHOR 3D map of BG505 SOSIP v5.2 N241/N289 in complex with the polyclonal Fab pAbC-8 from animal Rh.33311 (Wk26 time point). Half-map 2