2025-07-02 REL PDBe 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 atom_site entity entity_name_com entity_poly entity_poly_seq entity_src_gen pdbx_poly_seq_scheme pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues struct_conf struct_conn struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet_range _atom_site.label_seq_id _entity.formula_weight _entity.pdbx_description _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_src_gen.gene_src_common_name _entity_src_gen.pdbx_end_seq_num _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _struct_conf.beg_label_seq_id _struct_conf.end_label_seq_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_label_seq_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref_seq.db_align_beg _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end _struct_ref_seq.seq_align_end _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_seq_id DATABASE_REFERENCES citation database_2 _citation.title _database_2.pdbx_DOI _database_2.pdbx_database_accession 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 PDBe PDBe 2020-11-23 2021-04-28 2021-04-28 2025-07-02 Hallberg BM Das H spike glycoprotein, SARS-CoV-2, nanobody, VIRAL PROTEIN Koenig PA Das H Liu H Kummerer BM Gohr FN Jenster LM Schiffelers LDJ Tesfamariam YM Uchima M Wuerth JD Gatterdam K Ruetalo N Christensen MH Fandrey CI Normann S Todtmann JMP Pritzl S Hanke L Boos J Yuan M Zhu X Schmid-Burgk JL Kato H Schindler M Wilson IA Geyer M Ludwig KU Hallberg BM Wu NC Schmidt FI Science US 371 2021 33436526 doi:10.1126/science.abe6230 1095-9203 0038 SCIEAS 7b14 FULLOVERLAP SARS-CoV-2 glycoprotein in complex with a nanobody named V SARS-CoV-2 glycoprotein in complex with a nanobody named V 0 1 2 0.51 Spike glycoprotein 1 1 Severe acute respiratory syndrome coronavirus 2 Nanobody against SARS-CoV-2 1 2 Camelus bactrianus Spike protein S1 Severe acute respiratory syndrome coronavirus 2 0.022002676 1 Homo sapiens LEVO TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAP GQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPL QSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPK P0DTC2 Nanobody against SARS-CoV-2 Camelus bactrianus 0.014109522999999999 1 Escherichia coli LEVO QVQLVETGGGFVQPGGSLRLSCAASGVTLDYYAIGWFRQAPGKEREGVSCIGSSDGRTYYSDSVKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCALTVGTYYSGNYHYTCSDDMDYWGKGTQVTVSS 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 1 NAG singleParticle particle 7.3 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 BIOQUANTUM (6k x 4k) 49.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION

Ab initio from CryoSparc

3.79 FSC 0.143 CUT-OFF cryoSPARC 2.15 38308 PROJECTION MATCHING PROJECTION MATCHING cryoSPARC 2.15 FLEXIBLE FIT REAL emd_11978_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 612.0 612.0 612.0 90.0 90.0 90.0 X Y Z -2.1662593 4.28976 -0.00032177666 0.26486188 1.02 1.02 1.02 AUTHOR ::::EMDATABANK.org::::EMD-11978:::: Half map 1 from localised reconstruction emd_11978_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 612.0 612.0 612.0 90.0 90.0 90.0 X Y Z -2.5026665 3.6879025 -0.00032377473 0.2814114 1.02 1.02 1.02 AUTHOR ::::EMDATABANK.org::::EMD-11978:::: Half map 2 from localised reconstruction