2024-11-20 REL RCSB RCSB RCSB 2020-01-05 2020-01-29 2020-07-22 2024-11-20 Bill & Melinda Gates Foundation OPP1115782 United States BG505-SOSIP model reconstructed by subparticle extraction and refinement from a tetrahedral nanoparticle T33_dn10 Antanasijevic A Ward AB Nanoparticle, Rosetta, De novo protein design, HIV Env, DE NOVO PROTEIN Antanasijevic A Ueda G Brouwer PJM Copps J Huang D Allen JD Cottrell CA Yasmeen A Sewall LM Bontjer I Ketas TJ Turner HL Berndsen ZT Montefiori DC Klasse PJ Crispin M Nemazee D Moore JP Sanders RW King NP Baker D Ward AB Structural and functional evaluation of de novo-designed, two-component nanoparticle carriers for HIV Env trimer immunogens. Plos Pathog. US 16 e1008665 e1008665 2020 32780770 doi:10.1371/journal.ppat.1008665 1553-7374 EMD-21185 other EM volume
BG505-SOSIP antigen was refined by subparticle extraction and refinement from a T33_dn10 nanoparticle dataset shown elsewhere.
 6vfl FULLOVERLAP BG505-SOSIP reconstructed from the tetrahedral nanoparticle T33_dn10 by subparticle extraction and refinement BG505-SOSIP reconstructed from the tetrahedral nanoparticle T33_dn10 by subparticle extraction and refinement 0 1 2
Nanoparticle is assembled by combining equimolar amounts of BG505-SOSIP-T33_dn10A and T33_dn10B and subsequent incubation. EM map of the full nanoparticle can be found elsewhere (D_1000246183). Signal originating from the nanoparticle was subtracted and BG505-SOSIP antigens are extracted as independent subparticles
synthetic construct BG505-SOSIPv5.2(7S) - gp120 synthetic construct 0.05686366799999999 3 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTD PNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELR DKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGP CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTVKSIRIGPGQWFYYT GDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNT SVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWR SELYKYKVVKIEPLGVAPTRCKRRVVG BG505-SOSIPv5.2(7S) - gp41 synthetic construct 0.017198387 3 Homo sapiens LEVO AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKDTHWGIKQLQARVLAVEHYLRDQQ LLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLELD 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 33 NAG singleParticle particle 1.6 7.4 25.0 Tris-HCl 150.0 NaCl sodium chloride
TBS buffer, pH 7.4
 Quantifoil R2/1 COPPER 400 CARBON HOLEY 11.0 PLASMA CLEANING OTHER ETHANE 100 283 FEI VITROBOT MARK IV
Blotting time varied in the 3-7 s range, Blotting force set to 0, Wait time of 10s..
Nanoparticle is assembled by combining equimolar amounts of BG505-SOSIP-T33_dn10A and T33_dn10B and subsequent incubation. Nanoparticle is purified from unassembled components by SEC. Sample is then concentrated to 1.6mg/ml in TBS buffer.
 FEI TALOS ARCTICA FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 70.0 2.7 0.6 2.0 36000.0 OTHER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 1 798 11.25 49.39 1 324420
81105 T33_dn10 tetrahedral nanoparticles (each carrying 4 copies of BG505-SOSIP antigen) have been 3D aligned in Relion. Particles have been aligned and refined using tetrahedral symmetry. Localized reconstruction v1.2 was then applied to extract the BG505-SOSIP trimeric subparticles, resulting in a total of 324420 starting particles. The full nanoparticle reconstruction can be found elsewhere (EMD-21185).
Ab Initio map from cryoSPARC
 1 C3 BACK PROJECTION 4.14 FSC 0.143 CUT-OFF RELION 3.0 84435 MAXIMUM LIKELIHOOD RELION 3.0
Particle 2D aligned in cryoSPARC and then in Relion
 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_21186.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 -0.09490436 0.16213804 0.0016676999 0.007868744 1.15 1.15 1.15 0.04 AUTHOR BG505-SOSIP subparticle reconstruction following extraction from BG505-SOSIP-T33_dn10 nanoparticle, CryoEM Map 5CEZ PDB experimental model RIGID BODY FIT
Model refinement was performed by iterating between Rosetta relaxed refinement and manual refinement in Coot.
REAL emd_21186_msk_1.map emd_21186_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 -0.008342703 0.048889928 0.0015985996 0.0041958396 1.15 1.15 1.15 AUTHOR BG505-SOSIP subparticle reconstruction following extraction from BG505-SOSIP-T33_dn10 nanoparticle, CryoEM Halfmap 2 emd_21186_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 -0.009427208 0.047416054 0.0015584531 0.0041838805 1.15 1.15 1.15 AUTHOR BG505-SOSIP subparticle reconstruction following extraction from BG505-SOSIP-T33_dn10 nanoparticle, CryoEM Halfmap 1