2025-06-04 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2022-02-17 2022-03-30 2022-03-30 2025-06-04 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States Local refinement of cryo-EM structure of the interface of the Omicron RBD in complex with antibodies B-182.1 and A19-46.1 Zhou T kwong PD antibody, SARS-CoV-2, Omicron, B.1.1.529, Receptor binding domain, IMMUNE SYSTEM, Vral Protein-IMMUNE SYSTEM complex Zhou T Wang L Misasi J Pegu A Zhang Y Harris DR Olia AS Talana CA Yang ES Chen M Choe M Shi W Teng IT Creanga A Jenkins C Leung K Liu T Stancofski ED Stephens T Zhang B Tsybovsky Y Graham BS Mascola JR Sullivan NJ Kwong PD Structural basis for potent antibody neutralization of SARS-CoV-2 variants including B.1.1.529. Science US 376 eabn8897 eabn8897 2022 35324257 doi:10.1126/science.abn8897 1095-9203 0038 SCIEAS 7u0d FULLOVERLAP Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1 Ternary complex of SARS-CoV-2 Omicron RBD in complex with antibodies B1-182.1 and A19-46.1 0 1 2 3 4 5 Homo sapiens Surface glycoprotein Severe acute respiratory syndrome coronavirus 2 0.022297182 1 Homo sapiens LEVO NITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQI APGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYF PLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCG A0A7U3CI26 Heavy chain of SARS-CoV-2 antibody A19-46.1 Homo sapiens 0.0248699 1 Homo sapiens LEVO QVQLVESGGGVVQPGRSLRLSCAASGFTLSSYGMHWVRQAPGKGLEWVAVISYDGSNKYYVDSVKGRFTISRDNSKNTLY LQMNSLRAEDTAVYYCARGWAYWELLPDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFP EPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK Light chain of SARS-CoV-2 antibody A19-46.1 Homo sapiens 0.022760273 1 Homo sapiens LEVO QTVVTQEPSFSVSPGGTVTLTCGLSSGSVSTAYFPSWYQQTPGQAPRTLIYGTNTRSSGVPDRFSGSILGNKAALTITGA QADDESDYYCVLYMGRGIVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVK AGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS Heavy chain of SARS-CoV-2 antibody B1-182.1 Homo sapiens 0.024285312 1 Homo sapiens LEVO QMQLVQSGPEVKKPGTSVKVSCKASGFTFTSSAVQWVRQARGQRLEWIGWIVVGSGNTNYAQKFQERVTITRDMSTSTAY MELSSLRSEDTAVYYCAAPYCSGGSCFDGFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK Light chain of SARS-CoV-2 antibody B1-182.1 Homo sapiens 0.023536008 1 Homo sapiens LEVO EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGFPDRFSGSGSGTDFTLTISRLE PEDFAVYYCQQYGNSPWTFGQGTKVEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNS QESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 0.5 7.4
100 mM HEPES, 150 mM NaCl
 Quantifoil R1.2/1.3 COPPER GLOW DISCHARGE ETHANE 95 277 FEI VITROBOT MARK IV
Blot for 2-3.5 seconds before plugging..
Complex at 0.5 mg/mL concentration in the buffer
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 100.0 2.7 1.0 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K3 (6k x 4k) 40.0 1 46244
SARS-CoV-2 receptor-binding domain in complex with antibodies B1-182.1 and A19-46.1
 cryoSPARC 3 PHASE FLIPPING AND AMPLITUDE CORRECTION 7TCC 4.8 FSC 0.5 CUT-OFF 46244 NOT APPLICABLE NOT APPLICABLE emd_26256.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -0.40156403 0.87982863 -0.0009964088 0.011409314 0.855 0.855 0.855 0.235 AUTHOR Local refinement map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1 emd_26256_msk_1.map emd_26256_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -0.83711654 1.4575126 -0.0009964088 0.017742855 0.855 0.855 0.855 AUTHOR Sharpened local refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1 emd_26256_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -0.9509336 1.3598547 -0.00038870238 0.102783255 0.855 0.855 0.855 AUTHOR Local refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1 emd_26256_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 513.0 513.0 513.0 90.0 90.0 90.0 X Y Z -0.8395835 1.368702 -0.00037043574 0.10308633 0.855 0.855 0.855 AUTHOR Local refinement half map for the interface of Omicron RBD in complex with Fab B1-182.1 and Fab A19-46.1