2024-11-13 REL RCSB RCSB RCSB 2021-02-17 2021-07-14 2021-07-14 2024-11-13 Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody A23-58.1 that targets the receptor-binding domain Zhou T Tsybovsky Y SARS-CoV-2, Receptor-binding domain, antibody, VIRAL PROTEIN-IMMUNE SYSTEM complex Wang L Zhou T Zhang Y Yang ES Schramm CA Shi W Pegu A Oloniniyi OK Henry AR Darko S Narpala SR Hatcher C Martinez DR Tsybovsky Y Phung E Abiona OM Antia A Cale EM Chang LA Choe M Corbett KS Davis RL DiPiazza AT Gordon IJ Hait SH Hermanus T Kgagudi P Laboune F Leung K Liu T Mason RD Nazzari AF Novik L O'Connell S O'Dell S Olia AS Schmidt SD Stephens T Stringham CD Talana CA Teng IT Wagner DA Widge AT Zhang B Roederer M Ledgerwood JE Ruckwardt TJ Gaudinski MR Moore PL Doria-Rose NA Baric RS Graham BS McDermott AB Douek DC Kwong PD Mascola JR Sullivan NJ Misasi J Ultrapotent antibodies against diverse and highly transmissible SARS-CoV-2 variants. Science US 373 2021 34210892 doi:10.1126/science.abh1766 1095-9203 0038 SCIEAS EMD-23499 other EM volume
Full spike with antibody
 EMD-23915 other EM volume
Structure from same class member
 7lrs FULLOVERLAP SARS-CoV-2 spike in complex with neutralizing antibody A789-58.1 SARS-CoV-2 spike in complex with neutralizing antibody A789-58.1 0 1 2 3
The complex was prepared by mixing SARS-CoV-2 spike protein and Fab fragment of antibody A789-58.1 at a molar ratio of 1:3.6.
Severe acute respiratory syndrome coronavirus 2 0.539951 Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.021986652 1 Homo sapiens LEVO ITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIA PGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFP LQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGP P0DTC2 antibody A23-58.1 heavy chain Homo sapiens 0.024363425999999997 1 Homo sapiens LEVO QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAY MELSSLRSEDTAVYYCAAPNCSNVVCYDGFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK antibody A23-58.1 light chain Homo sapiens 0.023475006 1 Homo sapiens LEVO EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYSASSRATGIPDRFSGSGSGTDFTLTISRLE PEDFAVYFCQQYGTSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC singleParticle particle 0.5 7.4
100 mM HEPES, pH 7.4, 150 mM NaCl
 ETHANE 95 277 FEI VITROBOT MARK IV
Blot for 1.5 seconds before plugging..
Complex at 0.5 mg/mL concentration in the presence of 0.005% DDM
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.1 2.1 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN OTHER 40.0 1
Local refinement of the SARS-CoV-2 RBD region in complex with the antibody A789-58.1 Fab
123016
Particle subtraction from the spike-Fab complex
 7KMS 1 FOURIER SPACE 3.89 FSC 0.5 CUT-OFF 123016 NOT APPLICABLE NOT APPLICABLE emd_23498.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 437.76 437.76 437.76 90.0 90.0 90.0 X Y Z -0.18252574 0.8594941 -0.0006386036 0.005896388 0.855 0.855 0.855 0.11 AUTHOR 7KMS PDB experimental model OTHER REAL emd_23498_msk_1.map emd_23498_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 437.76 437.76 437.76 90.0 90.0 90.0 X Y Z -0.37177163 1.3092911 -0.0006386036 0.007696021 0.855 0.855 0.855 AUTHOR emd_23498_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 437.76 437.76 437.76 90.0 90.0 90.0 X Y Z -1.121062 1.9502363 -0.00018932928 0.12608796 0.855 0.855 0.855 AUTHOR emd_23498_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 437.76 437.76 437.76 90.0 90.0 90.0 X Y Z -1.0188434 1.5242748 -0.00019706816 0.12631124 0.855 0.855 0.855 AUTHOR