2020-11-25 REL RCSB RCSB RCSB 2020-01-05 2020-01-29 2020-07-22 2020-11-25 Bill & Melinda Gates Foundation OPP1115782 United States BG505-SOSIP map reconstructed by subparticle extraction and refinement from an icosahedral nanoparticle (I53_dn5) Ward AB Antanasijevic A 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-21183 other EM volume
Subparticles were extracted from the nanoparticle dataset reported in this entry.
 EMD-21184 associated EM volume BG505-SOSIP reconstructed from the icosahedral nanoparticle I53_dn5 by subparticle extraction and refinement BG505-SOSIP reconstructed from the icosahedral nanoparticle I53_dn5 by subparticle extraction and refinement 0 1 2
Nanoparticle is assembled by combining equimolar amounts of BG505-SOSIP-I53_dn5B and I53_dn5A and subsequent incubation. EM map of the full nanoparticle can be found elsewhere (D_1000246150).
synthetic construct BG505-SOSIP-I53_dn5B synthetic construct Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTDPNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGPCTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTVKSIRIGPGQWFYYTGDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPECQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQGSGSGSGSGGEEAELAYLLGELAYKLGEYRIAIRAYRIALKRDPNNAEAWYNLGNAYYKQGRYREAIEYYQKALELDPNNAEAWYNLGNAYYERGEYEEAIEYYRKALRLDPNNADAMQNLLNAKMREELEAS I53_dn5A synthetic construct LEVO MGKYDGSKLRIGILHARWNAEIILALVLGALKRLQEFGVKRENIIIETVPGSFELPYGSKLFVEKQKRLGKPLDAIIPIGVLIKGSTMHFEYICDSTTHQLMKLNFELGIPVIFGVLTCLTDEQAEARAGLIEGKMHNHGEDWGAAAVEMATKFNLEHHHHHH singleParticle particle 1.7 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-I53_dn5B and I53_dn5A and subsequent incubation. Nanoparticle is purified from unassembled components by SEC. Sample is then concentrated to 1.7mg/ml in TBS buffer.
 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 2 2999 11.25 49.39 1 515820
25791 I53_dn5 nanoparticles have been picked manually in Relion. Particles have been aligned and refined using icosahedral symmetry. Localized reconstruction v1.2 was then applied to extract the BG505-SOSIP trimeric subparticles (20 per nanoparticle), resulting in a total of 515820 starting particles. The full nanoparticle reconstruction can be found elsewhere: EMD-21183.
 RELION 3.0
Ab Initio map from cryoSPARC
 1 C3 BACK PROJECTION 6.68 FSC 0.143 CUT-OFF RELION 3.0
The reconstruction reported here is just of the BG505-SOSIP subparticles. The full BG505-SOSIP-I53_dn5 nanoparticle reconstruction can be found elsewhere: EMD-21183.
7737 MAXIMUM LIKELIHOOD RELION 3.0
Particle 2D aligned in cryoSPARC and then in Relion
 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_21184.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 -0.011629296 0.04818793 0.0014573443 0.004679265 1.15 1.15 1.15 0.025 AUTHOR BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM map
Model refinement was not performed due to low resolution.
 emd_21184_msk_1.map emd_21184_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 -0.016703108 0.043380905 0.001366898 0.0043783328 1.15 1.15 1.15 AUTHOR BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM Half-map 2 emd_21184_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 -0.018023197 0.048844237 0.0013919394 0.0047081686 1.15 1.15 1.15 AUTHOR BG505-SOSIP reconstructed as a subparticle from BG505-SOSIP-I53_dn5 nanoparticle, CryoEM Half-map 1