2024-10-23 REL RCSB RCSB RCSB 2021-02-21 2021-03-24 2021-03-24 2024-10-23 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) AI145687 United States Cryo-EM map of DH851.3 bound to HIV-1 CH505 Env Edwards RJ Manne K Acharya P Fab-dimerized, glycan-reactive, antibodies, HIV-1, DH898.1, Fab-dimer, glycan-reactive neutralizing antibody, macaque HIV-1 vaccine-induced, B cell lineage, VIRAL PROTEIN-IMMUNE SYSTEM complex Williams WB Meyerhoff RR Edwards RJ Li H Manne K Nicely NI Henderson R Zhou Y Janowska K Mansouri K Gobeil S Evangelous T Hora B Berry M Abuahmad AY Sprenz J Deyton M Stalls V Kopp M Hsu AL Borgnia MJ Stewart-Jones GBE Lee MS Bronkema N Moody MA Wiehe K Bradley T Alam SM Parks RJ Foulger A Oguin T Sempowski GD Bonsignori M LaBranche CC Montefiori DC Seaman M Santra S Perfect J Francica JR Lynn GM Aussedat B Walkowicz WE Laga R Kelsoe G Saunders KO Fera D Kwong PD Seder RA Bartesaghi A Shaw GM Acharya P Haynes BF Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 184 2955 2021 34019795 doi:10.1016/j.cell.2021.04.042 1097-4172 Acharya P Williams W Henderson R Janowska K Manne K Parks R Deyton M Sprenz J Stalls V Kopp M Mansouri K Edwards RJ Meyerhoff RR Oguin T Sempowski G Saunders K Haynes BF Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques bioRxiv US 2020 doi:10.1101/2020.06.30.178921 2692-8205 EMD-23519 other EM volume
Cryo-EM structure of DH898.1 Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer.
 7lu9 FULLOVERLAP DH851.3 bound to HIV-1 CH505 Env DH851.3 bound to HIV-1 CH505 Env 0 1 2 3 4 5 6 Human immunodeficiency virus 1 DH851.3 light chain Macaca mulatta 0.022127463 3 Homo sapiens LEVO ALTQPPSVSKSLEQSVTISCTGTTTGNSVSWYQCHSGTAPRLLIYDVNKRPSGVSDRFSGSKSHNTASLTIFGLQAEDEA DYYCGSYGSGGSLLFGGGTRLTVLGQP(UNK)KASPTVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGSAVNA GVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAPAEC DH851.3 heavy chain Macaca mulatta 0.024451617 3 Homo sapiens LEVO QVTLMESGPALVKVTQTLAVTCTFSGFSIRDSGKGVAWIRQPPGGALEWLTSIYWDDTKYHDTSLKPRLTIFRDTSQTQV ILILTNMAPLDTATYYCGRINNGGGWKDHIDFWGPGLLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPV TVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVEIKTCGG DH851.3 heavy chain Macaca mulatta 0.023890929999999998 3 Homo sapiens LEVO QVTLMESGPALVKVTQTLAVTCTFSGFSIRDSGKGVAWIRQPPGGALEWLTSIYWDDTKYHDTSLKPRLTIFRDTSQTQV ILILTNMAPLDTATYYCGRINNGGGWKDHIDFWGPGLLVTVSSASTKGPSVFPLAPSSRSTSESTAALGCLVKDYFPEPV TVSWNSGSLTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYVCNVNHKPSNTKVDKRVE DH851.3 light chain Macaca mulatta 0.021824127 3 Homo sapiens LEVO ALTQPPSVSKSLEQSVTISCTGTTTGNSVSWYQCHSGTAPRLLIYDVNKRPSGVSDRFSGSKSHNTASLTIFGLQAEDEA DYYCGSYGSGGSLLFGGGTRLTVLGQP(UNK)KASPTVTLFPPSSEELQANKATLVCLISDFYPGVVKVAWKADGSAVNA GVETTTPSKQSNNKYAASSYLSLTSDQWKSHKSYSCQVTHEGSTVEKTVAP Envelope glycoprotein gp41 Human immunodeficiency virus 1 0.017134511999999998 3 Homo sapiens LEVO AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLKAIEAQQHLLKLTVWGIKQLQARVLAVERYLRDQQ LLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQWDKEISNYTQIIYGLLEESQNQQEKNEQDLLALD Envelope glycoprotein gp120 Human immunodeficiency virus 1 0.051898061999999995 3 Homo sapiens LEVO ENLWVTVYYGVPVWKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLKNVTENFNMWKNDMVDQMHEDVISL WDQSLKPCVKLTPLCVTLNCTNATASNSSIIEGMKNCSFNITTELRDKREKKNALFYKLDIVQLDGNSSQYRLINCNTSV ITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFTGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEGEIIIRSENITNN VKTIIVHLNESVKIECTRPNNKTRTSIRIGPGQWFYATGQVIGDIREAYCNINESKWNETLQRVSKKLKEYFPHKNITFQ PSSGGDLEITTHSFNCGGEFFYCNTSSLFNRTYMANSTDMANSTETNSTRTITIHCRIKQIINMWQEVGRAMYAPPIAGN ITCISNITGLLLTRDGGKNNTETFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTRCKRRV M4M097 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 7.5 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE AIR ETHANE 95 293 LEICA EM GP
blot for 2.5 seconds before plunging.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 93.15 93.15 GATAN K3 (6k x 4k) 6058 62.0 1 5.6 FSC 0.143 CUT-OFF cryoSPARC 53398 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC emd_23518.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 232 223 141 75 98 121 141 223 232 150.3765 237.82948 247.428 90.0 90.0 90.0 Z Y X -0.4758269 0.89355016 0.000000000000366 0.040937867 1.0665 1.0665 1.0665 0.05 EMDB CryoEM map of DH851.3 bound to HIV-1 CH505 Env AB INITIO MODEL emd_23518_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 409.53598 409.53598 409.53598 90.0 90.0 90.0 X Y Z -0.68440026 0.9739723 0.0018824231 0.09050466 1.0665 1.0665 1.0665 AUTHOR CryoEM half-map A of DH851.3 bound to HIV-1 CH505 Env emd_23518_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 409.53598 409.53598 409.53598 90.0 90.0 90.0 X Y Z -0.61997783 0.9911825 0.0018009318 0.09022899 1.0665 1.0665 1.0665 AUTHOR CryoEM half-map B of DH851.3 bound to HIV-1 CH505 Env