Cryo-EM reconstruction of B41 SOSIP.664 in complex with fragment antigen binding of b12

2024-12-25 REL RCSB RCSB RCSB 2017-04-28 2017-07-12 2017-07-12 2024-12-25 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) UM1AI100663 United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) P01 AI110657 United States Cryo-EM reconstruction of B41 SOSIP.664 in complex with fragment antigen binding of b12 Pallesen J Ozorowski G de Val N Ward AB neutralizing antibody, HIV-1, envelope glycoprotein, receptor binding site, IMMUNE SYSTEM Ozorowski G Pallesen J de Val N Lyumkis D Cottrell CA Torres JL Copps J Stanfield RL Cupo A Pugach P Moore JP Wilson IA Ward AB Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature UK 547 360 363 2017 28700571 doi:10.1038/nature23010 1476-4687 0006 NATUAS EMD-8716 other EM volume EMD-8715 other EM volume EMD-8714 other EM volume EMD-8713 other EM volume 5vn8 FULLOVERLAP HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding HIV-1 Env B41 SOSIP.664 in complex with b12 fragment antigen binding 0 1 2 3 4 0.57 HIV-1 Env B41 SOSIP.664 1 1 2 Human immunodeficiency virus 1 b12 fragment 1 3 4 Homo sapiens Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.05770246899999999 3 Homo sapiens LEVO MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARAAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACV PTDPNPQEIVLGNVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWEKMET GEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSVITQACPKVSFEPIPIHYCAPAGFA ILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTR KSIHIGPGRAFYATGDIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEFFYCN TTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRCSSNITGLLLTRDGGRDQNGTETFR PGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV B3UES2 Envelope glycoprotein gp160 Human immunodeficiency virus 1 0.017357824 3 Homo sapiens LEVO AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVWGIKQLQARVLAVERYLRDQQ LLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQWEKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD B3UEZ6 b12 Fab heavy chain Homo sapiens 0.024910846 3 Homo sapiens LEVO QVQLVQSGAEVKKPGASVKVSCQASGYRFSNFVIHWVRQAPGQRFEWMGWINPYNGNKEFSAKFQDRVTFTADTSANTAY MELRSLRSADTAVYYCARVGPYSWDDSPQDNYYMDVWGKGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYF PEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC b12 Fab light chain Homo sapiens 0.023707354 3 Homo sapiens LEVO EIVLTQSPGTLSLSPGERATFSCRSSHSIRSRRVAWYQHKPGQAPRLVIHGVSNRASGISDRFSGSGSGTDFTLTITRVE PEDFALYYCQVYGASSYTFGQGTKLERKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 33 NAG singleParticle particle 5 7.4 150.0 NaCl sodium chloride 50.0 Tris 0.06 DDM

DDM was added to a final concentration of 0.06 mM prior to vitrification

C-flat-2/2 COPPER 300 CARBON HOLEY PLASMA CLEANING 10 OTHER ETHANE 277 HOMEMADE PLUNGER

3 uL of sample applied to a holey carbon grid on glow discharged face and blotted manually on sample side until filter paper detached from grid, followed by immediate plunging.

B41 SOSIP.664 was incubated with a 6X molar excess of 17b Fab overnight at room temperature, purified by size exclusion chromatography, and concentrated prior to grid application

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 1.0 4.0 22500.0 38168.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 4096 4096 1-50 1300 10.0 58.0 1 C3 3.6 FSC 0.143 CUT-OFF RELION 2.0 88071 PROJECTION MATCHING 7.5 RELION 2.0 PROJECTION MATCHING 0.94 RELION 2.0 RELION 2.0 emd_8717.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.20810786 0.39907405 0.00026210453 0.010594209 1.31 1.31 1.31 0.08 AUTHOR ::::EMDATABANK.org::::D_1000227686:::: Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12 FLEXIBLE FIT

Homology model of B41 SOSIP.664 created using PDB 5CEZ as initial model. b12 coordinates taken from PDB 2NY7. Performed fragment based refinement using Rosetta, followed by relaxed refinement in Rosetta. Modeled glycans using Chimera and performed final refinements using Phenix.

EMRinger REAL emd_8717_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.04214821 0.1532893 0.00026210453 0.0066283722 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::D_1000227686:::: Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, additional map emd_8717_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.013944946 0.069294214 0.00013454111 0.0032105986 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::D_1000227686:::: Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, half-map emd_8717_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 335.36 335.36 335.36 90.0 90.0 90.0 X Y Z -0.013944946 0.069294214 0.00013454111 0.0032105986 1.31 1.31 1.31 AUTHOR ::::EMDATABANK.org::::D_1000227686:::: Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain of b12, half-map