2024-11-06 REL RCSB RCSB RCSB 2020-12-30 2021-08-04 2021-08-04 2024-11-06 International AIDS Vaccine Initiative OPP1196345 United States BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) Antanasijevic A Froes Rocha R HIV, vaccine design, protein design, nanoparticles, BG505, VIRAL PROTEIN 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 7l7u FULLOVERLAP BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) 0 1 2
The map was generated by subparticle extraction from the BG505 SOSIP-T33-31 nanoparticle using the localized reconstruction approach.
Human immunodeficiency virus 1 BG505 SOSIP.v5.2(7S) - gp120 Human immunodeficiency virus 1 0.05670748 3 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTD PNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELR DKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGP CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTVKSIRIGPGQWFYYT GDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNT SVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWR SELYKYKVVKIEPLGVAPTRCKRRV BG505 SOSIP.v5.2(7S) - gp41 Human immunodeficiency virus 1 0.016543626999999998 3 Homo sapiens LEVO LGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCS GKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLELD 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 39 NAG singleParticle particle 4.1 7.4 20.0 Tris-HCl 150.0 NaCl Sodium chloride
TBS buffer prepared from a 10X stock
 Quantifoil R2/1 COPPER 400 CARBON HOLEY PLASMA CLEANING OTHER ETHANE 100 283 FEI VITROBOT MARK IV
Blotting time varied between 3 and 7 seconds..
BG505 SOSIP-T33-31 nanoparticle was prepared by combining equimolar amounts of BG505 SOSIP-T33-31A and BG505 SOSIP-T33-31B components that were expressed separately.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.8 2.0 36000.0 OTHER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1-41 2 1751 10.25 50.0 1
Frames were aligned using MotionCorr and GCTF was applied for estimation of CTF parameters.
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Subparticles were generated by extraction from 110,369 BG505 SOSIP-T33-31 nanoparticles (4 subparticles per 1 nanoparticle).
Map obtained from Ab initio reconstruction in cryoSPARC
 C3 BACK PROJECTION 3.8 FSC 0.143 CUT-OFF RELION 3.0 64726 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_23219.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 207.0 207.0 207.0 90.0 90.0 90.0 X Y Z -0.1494741 0.23227064 0.0022507317 0.010273769 1.15 1.15 1.15 0.03 AUTHOR BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Main map 6VL5 PDB experimental model RIGID BODY FIT REAL emd_23219_msk_1.map emd_23219_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 207.0 207.0 207.0 90.0 90.0 90.0 X Y Z -0.016349804 0.058684547 0.0018480223 0.0048772614 1.15 1.15 1.15 AUTHOR BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Half-map 2 emd_23219_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 180 180 180 0 0 0 180 180 180 207.0 207.0 207.0 90.0 90.0 90.0 X Y Z -0.019984739 0.05951687 0.0024127432 0.004836479 1.15 1.15 1.15 AUTHOR BG505 SOSIP reconstructed from a designed nanoparticle, BG505 SOSIP-T33-31 (Component B) - Half-map 1