2025-05-21 REL RCSB 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 DATABASE_REFERENCES citation _citation.journal_volume 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 RCSB RCSB 2020-09-29 2021-09-29 2021-09-29 2025-05-21 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) HHSN272201700060C United States National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 75N93019C00062 United States SARS-CoV-2 Spike in complex with neutralizing Fab 2B04 (one up, two down conformation) Errico JM Fremont DH SARS-CoV-2, Neutralizing antibody, ACE2-competitive, Receptor-binding domain, VIRAL PROTEIN-IMMUNE SYSTEM complex, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID Errico JM Zhao H Chen RE Liu Z Case JB Ma M Schmitz AJ Rau MJ Fitzpatrick JAJ Shi PY Diamond MS Whelan SPJ Ellebedy AH Fremont DH Structural mechanism of SARS-CoV-2 neutralization by two murine antibodies targeting the RBD. Cell Rep US 37 109881 109881 2021 34655519 doi:10.1016/j.celrep.2021.109881 2211-1247 EMD-22749 other EM volume EMD-22750 other EM volume EMD-22751 other EM volume EMD-22752 other EM volume EMD-22753 other EM volume 7k9h FULLOVERLAP Complex of SARS-CoV-2 Spike with Fab fragments of neutralizing antibody 2B04 Complex of SARS-CoV-2 Spike with Fab fragments of neutralizing antibody 2B04 0 1 2 3
Fab fragments generated by proteolytic cleavage of recombinantly expressed IgG
 SARS-CoV-2 Spike 1 1 Severe acute respiratory syndrome coronavirus 2 Fab fragment of neutralizing monoclonal antibody 2B04 1 2 3 Homo sapiens Spike glycoprotein Severe acute respiratory syndrome coronavirus 2 0.139316375 3 Homo sapiens LEVO MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFD NPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVY SSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQT LLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRV QPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSF VIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPC NGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFL PFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGS NVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPASVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVT TEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFS QILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTIT SGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLV KQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFC GKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVS GNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL GKYEQYIKWPSGRLVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH P0DTC2 2B04 heavy chain Mus musculus 0.013162778 2 Homo sapiens LEVO QVQLKQSGPGLVAPSQSLSITCTVSGFSLINYAISWVRQPPGKGLEWLGVIWTGGGTNYNSALKSRLSISKDNSKSQVFL KMNSLQTDDTARYYCARKDYYGRYYGMDYWGQGTSVTVS 2B04 light chain Mus musculus 0.011530766 2 Homo sapiens LEVO QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGA QTEDEAIYFCALWYNNHWVFGGGTKLTVL 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG singleParticle particle 1.0 7.5 20.0 C8H18N2O4S HEPES 150.0 NaCl sodium chloride 0.01 NaN3 Sodium Azide COPPER 300 GLOW DISCHARGE AIR
15mA
 ETHANE 100 298 FEI VITROBOT MARK IV
20s wait time 2s blot time.
0.2 7.5 20.0 C8H18N2O4S HEPES 150.0 NaCl sodium chloride 0.01 NaN3 Sodium Azide COPPER 300 GLOW DISCHARGE AIR
15mA
 ETHANE 100 298 FEI VITROBOT MARK IV
20s wait time 2s blot time.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.01 0.5 2.5 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN 80.0 80.0 Microscope was modified with a Cs corrector. GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) COUNTING 3838 3710 1-45 9.0 67.0 1 1842978 Gctf 1.06 PHASE FLIPPING AND AMPLITUDE CORRECTION 6VYB C1 3.2 FSC 0.143 CUT-OFF cryoSPARC 2.15 162281 MAXIMUM LIKELIHOOD RELION 3.1 MAXIMUM LIKELIHOOD RELION 3.1 RELION 3.1 emd_22748.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -1.6689818 2.9672728 0.0020975915 0.076256655 1.1 1.1 1.1 0.25 AUTHOR SARS-CoV-2 trimeric spike bound by Fab 2B04 REAL emd_22748_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -1.3442549 1.9588293 0.0027896496 0.16664527 1.1 1.1 1.1 AUTHOR Half map A emd_22748_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 330.0 330.0 330.0 90.0 90.0 90.0 X Y Z -1.4085472 1.9893082 0.0028147583 0.1665507 1.1 1.1 1.1 AUTHOR Half map B