2024-11-13 REL PDBe PDBe PDBe 2023-07-10 2023-11-01 2023-11-01 2024-11-13 Swiss National Science Foundation Switzerland XBB 1.0 RBD bound to P4J15 (Local) Duhoo Y Lau K SARS-Cov2, CryoEM, RBD-binding, FAB, VIRAL PROTEIN Fenwick C Turelli P Duhoo Y Lau K Herate C Marlin R Lamrayah M Campos J Esteves-Leuenberger L Farina A Raclot C Genet V Fiscalini F Cesborn J Perez L Dereuddre-Bosquet N Contreras V Lheureux K Relouzat F Abdelnabi R Leyssen P Levy Y Pojer F Le Grand R Trono D Pantaleo G Broadly potent anti-SARS-CoV-2 antibody shares 93% of epitope with ACE2 and provides full protection in monkeys. J Infect 87 524 537 2023 37852477 doi:10.1016/j.jinf.2023.10.008 1532-2742 8pq2 FULLOVERLAP Spike XBB.1 RBD up - P4J15 Fab (local) Spike XBB.1 RBD up - P4J15 Fab (local) 0 1 2 3
local refinement from the Full XBB.1 spike and RBD complex.
Severe acute respiratory syndrome coronavirus 2 72 P4J15 Fragment Antigen-Binding Heavy Chain Homo sapiens 0.013375937 1 Cricetulus griseus LEVO QVQIQQWGAGLLKPSETLSLTCAVYDESFSDYFWTWIRQSPGMGLEWIGEVTHTGSANYNPSLMSRVTMSRDTSKNQISL KLTSVTAADTAVYYCARDSPLGSIIKRGDYWGQGTLVTVSS P4J15 Fragment Antigen-Binding Light Chain Homo sapiens 0.01176199 1 Cricetulus griseus LEVO DIQMTQSPSSLSASVGDRVTVTCQASQGITNYVNWYQQKPGKAPKLLIYHASHLETGVPSRFSGSGSGTDFTFTISSLQP EDFATYYCQQFDHLPPTFGQGTRLEIK Spike protein S2' Severe acute respiratory syndrome coronavirus 2 0.021900671999999996 1 Cricetulus griseus LEVO TNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAP GQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGSNCYSPL QSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGP P0DTC2 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 2 7.4 0.137 NaCL Sodium Chloride 0.0027 KCl Potassium Chloride 0.01 Na2HPO4 Sodium Phosphate Dibasic 0.0018 KH2PO4 Potassium Phophate Monobasic Quantifoil R1.2/1.3 GOLD 300 CARBON HOLEY 10.0 GLOW DISCHARGE AIR ETHANE 95 283 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.0 96000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN FEI FALCON IV (4k x 4k) 50.0 1 6769807 1 C1 3.85 FSC 0.143 CUT-OFF cryoSPARC 4.1 95910 ANGULAR RECONSTITUTION cryoSPARC 4.1 ANGULAR RECONSTITUTION cryoSPARC 4.1 1 362329.0 cryoSPARC 4.1 emd_17819.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 456.51602 456.51602 456.51602 90.0 90.0 90.0 X Y Z -0.68942523 1.4194535 -0.00036630814 0.017610706 1.2681 1.2681 1.2681 0.2 AUTHOR AlphaFold in silico model FLEXIBLE FIT REAL emd_17819_msk_1.map emd_17819_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 456 456 456 0 0 0 456 456 456 578.2536 578.2536 578.2536 90.0 90.0 90.0 X Y Z -0.12300178 14.572993 -0.042837862 0.1600263 1.2681 1.2681 1.2681 AUTHOR Enhanced map using EMready. emd_17819_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 456.51602 456.51602 456.51602 90.0 90.0 90.0 X Y Z -0.5635428 1.0018197 0.00021377233 0.05776371 1.2681 1.2681 1.2681 AUTHOR emd_17819_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 456.51602 456.51602 456.51602 90.0 90.0 90.0 X Y Z -0.70363665 1.0827776 0.00021364499 0.05768388 1.2681 1.2681 1.2681 AUTHOR