2025-05-21 REL RCSB 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 DATA_COLLECTION em_admin em_software _em_admin.last_update _em_software.name RCSB RCSB 2022-07-18 2023-08-02 2023-08-02 2025-05-21 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01 AI165947 United States Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain Stalls V May AJ Acharya P SARS-CoV-2, VIRAL PROTEIN, Antibody, Fab, RBD, VIRAL PROTEIN-Immune System complex Stalls V Acharya P May AJ Malewana D Local refinement of SARS-CoV-2 vaccine induced antibody Ab026500 bound to SARS-CoV-2 HexaPro RBD Spike ectodomain To Be Published 0353 EMD-27606 other EM volume
Trimer map
 8dpz FULLOVERLAP Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike S1 local refinement Ab026500 Fab bound to SARS-CoV-2 HexaPro Spike S1 local refinement 0 1 2 3 Severe acute respiratory syndrome coronavirus 2 0.557 Spike protein S1 Severe acute respiratory syndrome coronavirus 2 0.023059967 1 Homo sapiens LEVO IVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGD EVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEG FNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKS P0DTC2 DH1338 Fab Heavy Chain Macaca mulatta 0.013910355999999999 1 Homo sapiens LEVO QLQLQESGPGLVKPSETLSLTCAVSGGSISRKNWSWIRQPPGKGLGWIGRISGSGGSTDYNPSLKSRVTISTDTSKNQFS LKLSSVTAADTAVYYCARVAYYEDDYGYYYTEGAFDFWGQGLRVTVSS DH1338 Fab Light Chain Macaca mulatta 0.011864079999999999 1 Homo sapiens LEVO EIVMTQSPATLSLSPGERATLSCRTSQSVSSYVAWYQQKPEQTPRLLIYDASSRATGIPDRFSGGGSGTDFTLTISSLEP EDFAVYYCQQYSNWPWTFGQGTKVEIK singleParticle particle 1.5 8.0 Quantifoil R1.2/1.3 COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 95 LEICA EM GP
Fab to spike 6:1 ratio.
 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.7000000000000001 2.5 NITROGEN GATAN K3 (6k x 4k) 1 7866 59.4 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 3.38 FSC 0.143 CUT-OFF Coot ISOLDE PHENIX 1103016 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 emd_27644.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -7.304406 15.7961645 -0.016831916 0.10738336 1.08 1.08 1.08 1.76 AUTHOR Sharp map from homogeneous C1 refinement in cryosparc 7LD1 PDB experimental model 3Q6G PDB experimental model FLEXIBLE FIT emd_27644_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -1.4004211 3.2903252 -0.0026552093 0.06708691 1.08 1.08 1.08 AUTHOR Half B map from homogeneous C1 refinement in cryosparc emd_27644_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 324.0 324.0 324.0 90.0 90.0 90.0 X Y Z -1.4620583 3.3581247 -0.0026184241 0.06708741 1.08 1.08 1.08 AUTHOR Half A map from homogeneous C1 refinement in cryosparc