2024-03-06 REL RCSB RCSB RCSB 2020-01-05 2020-01-29 2020-07-22 2024-03-06 Bill & Melinda Gates Foundation OPP1115782 United States De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface 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-21186 other EM volume
BG505-SOSIP in the related entry was reconstructed by subparticle extraction and refinement of this dataset.
 6vfk FULLOVERLAP De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface. Nanoparticle consists of 12 copies of both subunits (BG505-SOSIP-T33_dn10A and T33_dn10B) De novo designed tetrahedral nanoparticle T33_dn10 displaying 4 copies of BG505-SOSIP trimer on the surface. Nanoparticle consists of 12 copies of both subunits (BG505-SOSIP-T33_dn10A and T33_dn10B) 0 1 2
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
synthetic construct T33_dn10B synthetic construct 0.03146683 1 Escherichia coli BL21(DE3) LEVO MIEEVVAEMIDILAESSKKSIEELARAADNKTTEKAVAEAIEEIARLATAAIQLIEALAKNLASEEFMARAISAIAELAK KAIEAIYRLADNHTTDTFMARAIAAIANLAVTAILAIAALASNHTTEEFMARAISAIAELAKKAIEAIYRLADNHTTDKF MAAAIEAIALLATLAILAIALLASNHTTEKFMARAIMAIAILAAKAIEAIYRLADNHTSPTYIEKAIEAIEKIARKAIKA IEMLAKNITTEEYKEKAKKIIDIIRKLAKMAIKKLEDNRTLEHHHHHH BG505-SOSIP-T33_dn10A synthetic construct 0.088855289 1 Homo sapiens LEVO MKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAENLWVTVYYGVPVWKDAETTLFCASDAKAYETKKHNVWATHCCVPTD PNPQEIHLENVTEEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFNMTTELR DKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCKDKKFNGTGP CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIRSENITNNAKNILVQLNESVQINCTRPNNNTVKSIRIGPGQWFYYT GDIIGDIRQAHCNVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNSTWISNT SVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLILTRDGGSTNSTTETFRPGGGDMRDNWR SELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRRAVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRA PECQQHLLKDTHWGIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNY TQIIYGLLEESQNQQEKNEQGSGSGSGSGGEEAELAYLLGELAYKLGEYRIAIRAYRIALKRDPNNAEAWYNLGNAYYKQ GDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYEKALELDPENLEALQNLLNAMDKQG 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 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 25791
Template picking in cryoSPARC
Ab Initio map from cryoSPARC
 1 T BACK PROJECTION 4.25 FSC 0.143 CUT-OFF RELION 3.0 81105 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 RELION 3.0 emd_21185.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 506.0 506.0 506.0 90.0 90.0 90.0 X Y Z -0.044927433 0.08914533 0.000027195401 0.0026569706 1.15 1.15 1.15 0.022 AUTHOR De novo designed tetrahedral nanoparticle T33_dn10 presenting BG505-SOSIP, CryoEM Map RIGID BODY FIT
Model refinement was performed by iterative rounds of Rosetta relaxed refinement and manual refinement in Coot.
REAL emd_21185_msk_1.map emd_21185_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 506.0 506.0 506.0 90.0 90.0 90.0 X Y Z -0.008993126 0.04113571 0.000026285143 0.0017118504 1.15 1.15 1.15 AUTHOR De novo designed tetrahedral nanoparticle T33_dn10 presenting BG505-SOSIP, CryoEM Half-Map 1 emd_21185_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 440 440 440 0 0 0 440 440 440 506.0 506.0 506.0 90.0 90.0 90.0 X Y Z -0.008501077 0.041416958 0.000025197329 0.0017078625 1.15 1.15 1.15 AUTHOR De novo designed tetrahedral nanoparticle T33_dn10 presenting BG505-SOSIP, CryoEM Half-Map 2