A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors

2025-09-17 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY COORDINATE_REPLACEMENT AUTHOR Sequence discrepancy STRUCTURE_SUMMARY atom_site chem_comp_atom chem_comp_bond em_entity_assembly em_software entity entity_name_com entity_poly entity_poly_seq entity_src_gen ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_contact_author pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_conn_angle pdbx_struct_sheet_hbond pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues pdbx_validate_close_contact pdbx_validate_main_chain_plane pdbx_validate_peptide_omega pdbx_validate_rmsd_angle pdbx_validate_rmsd_bond pdbx_validate_torsion software struct struct_asym struct_conf struct_conn struct_mon_prot_cis struct_ref struct_ref_seq struct_ref_seq_dif struct_sheet struct_sheet_order struct_sheet_range _em_entity_assembly.entity_id_list _entity.formula_weight _entity.pdbx_description _entity.pdbx_ec _entity.pdbx_fragment _entity.pdbx_number_of_molecules _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.type _entity_src_gen.pdbx_end_seq_num _entity_src_gen.pdbx_gene_src_gene _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.sheet_id _pdbx_validate_main_chain_plane.improper_torsion_angle _pdbx_validate_peptide_omega.omega _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_value _struct.title _struct_asym.entity_id _struct_mon_prot_cis.pdbx_omega_angle _struct_ref.db_code _struct_ref.db_name _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _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.pdbx_db_accession _struct_ref_seq.pdbx_strand_id _struct_ref_seq.ref_id _struct_ref_seq.seq_align_beg _struct_ref_seq.seq_align_end _struct_sheet.number_strands _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.sense _struct_sheet_order.sheet_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_seq_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.id _struct_sheet_range.sheet_id STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification EXPERIMENTAL_SUMMARY em_admin em_software _em_admin.last_update _em_software.name DERIVED_CALCULATIONS em_admin pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBj PDBj 2022-09-16 2023-01-11 2023-01-11 2025-09-17 Ministry of Science and Technology (MoST, China) 2020YFA0707500 China Ministry of Science and Technology (MoST, China) 2017YFC0840300 China A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analogue inhibitors Yan LM Rao ZH Lou ZY SARS-CoV-2, capping, nucleotide analogue inhibitor, cryo-EM, VIRAL PROTEIN Yan L Huang Y Ge J Liu Z Lu P Huang B Gao S Wang J Tan L Ye S Yu F Lan W Xu S Zhou F Shi L Guddat LW Gao Y Rao Z Lou Z A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Cell 185 4347 4360.e17 2022 36335936 doi:10.1016/j.cell.2022.09.037 1097-4172 8gwe FULLOVERLAP EMDB EMD-34310 associated EM volume

E-RTC_RNA-nsp9_GMPPNP E-RTC_RNA-nsp9_GMPPNP 0 1 2 3 7 8 4 5 6 Severe acute respiratory syndrome coronavirus 2 RNA-directed RNA polymerase Severe acute respiratory syndrome coronavirus 2 0.106780977 1 Escherichia coli BL21(DE3) LEVO SADAQSFLNRVCGVSAARLTPCGTGTSTDVVYRAFDIYNDKVAGFAKFLKTNCCRFQEKDEDDNLIDSYFVVKRHTFSNY QHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRLTKYTMADLVYALRHFDEGNCDTLKEILVTYNCCDDDYFNKK DWYDFVENPDILRVYANLGERVRQALLKTVQFCDAMRNAGIVGVLTLDNQDLNGNWYDFGDFIQTTPGSGVPVVDSYYSL LMPILTLTRALTAESHVDTDLTKPYIKWDLLKYDFTEERLKLFDRYFKYWDQTYHPNCVNCLDDRCILHCANFNVLFSTV FPPTSFGPLVRKIFVDGVPFVVSTGYHFRELGVVHNQDVNLHSSRLSFKELLVYAADPAMHAASGNLLLDKRTTCFSVAA LTNNVAFQTVKPGNFNKDFYDFAVSKGFFKEGSSVELKHFFFAQDGNAAISDYDYYRYNLPTMCDIRQLLFVVEVVDKYF DCYDGGCINANQVIVNNLDKSAGFPFNKWGKARLYYDSMSYEDQDALFAYTKRNVIPTITQMNLKYAISAKNRARTVAGV SICSTMTNRQFHQKLLKSIAATRGATVVIGTSKFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLAR KHTTCCSLSHRFYRLANECAQVLSEMVMCGGSLYVKPGGTSSGDATTAYANSVFNICQAVTANVNALLSTDGNKIADKYV RNLQHRLYECLYRNRDVDTDFVNEFYAYLRKHFSMMILSDDAVVCFNSTYASQGLVASIKNFKSVLYYQNNVFMSEAKCW TETDLTKGPHEFCSQHTMLVKQGDDYVYLPYPDPSRILGAGCFVDDIVKTDGTLMIERFVSLAIDAYPLTKHPNQEYADV FHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHTVLQ P0DTD1 2.7.7.48 Non-structural protein 8 Severe acute respiratory syndrome coronavirus 2 0.021903047 2 Escherichia coli BL21(DE3) LEVO AIASEFSSLPSYAAFATAQEAYEQAVANGDSEVVLKKLKKSLNVAKSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKR AKVTSAMQTMLFTMLRKLDNDALNNIINNARDGCVPLNIIPLTTAAKLMVVIPDYNTYKNTCDGTTFTYASALWEIQQVV DADSKIVQLSEISMDNSPNLAWPLIVTALRANSAVKLQ P0DTD1 Replicase polyprotein 1a Severe acute respiratory syndrome coronavirus 2 0.008678143 1 Escherichia coli BL21(DE3) LEVO SKMSDVKCTSVVLLSVLQQLRVESSSKLWAQCVQLHNDILLAKDTTEAFEKMVSLLSVLLSMQGAVDINKLCEEMLDN P0DTC1 Helicase nsp13 Severe acute respiratory syndrome coronavirus 2 0.065989438 2 Escherichia coli BL21(DE3) LEVO AVGACVLCNSQTSLRCGACIRRPFLCCKCCYDHVISTSHKLVLSVNPYVCNAPGCDVTDVTQLYLGGMSYYCKSHKPPIS FPLCANGQVFGLYKNTCVGSDNVTDFNAIATCDWTNAGDYILANTCTERLKLFAAETLKATEETFKLSYGIATVREVLSD RELHLSWEVGKPRPPLNRNYVFTGYRVTKNSKVQIGEYTFEKGDYGDAVVYRGTTTYKLNVGDYFVLTSHTVMPLSAPTL VPQEHYVRITGLYPTLNISDEFSSNVANYQKVGMQKYSTLQGPPGTGKSHFAIGLALYYPSARIVYTACSHAAVDALCEK ALKYLPIDKCSRIIPARARVECFDKFKVNSTLEQYVFCTVNALPETTADIVVFDEISMATNYDLSVVNARLRAKHYVYIG DPAQLPAPRTLLTKGTLEPEYFNSVCRLMKTIGPDMFLGTCRRCPAEIVDTVSALVYDNKLKAHKDKSAQCFKMFYKGVI THDVSSAINRPQIGVVREFLTRNPAWRKAVFISPYNSQNAVASKILGLPTQTVDSSQGSEYDYVIFTQTTETAHSCNVNR FNVAITRAKVGILCIMSDRDLYDKLQFTSLEIP P0DTD1 3.6.4.12 Non-structural protein 9 Severe acute respiratory syndrome coronavirus 2 0.012391171 1 Escherichia coli BL21(DE3) LEVO NNELSPVALRQMSCAAGTTQTACTDDNALAYYNTTKGGRFVLALLSDLQDLKWARFPKSDGTGTIYTELEPPCRFVTDTP KGPKVKYLYFIKGLNNLNRGMVLGSLAATVRLQ P0DTD1 RNA (5'-R(P*AP*UP*UP*A)-3') Severe acute respiratory syndrome coronavirus 2 0.001225786 1 AUUA primer Severe acute respiratory syndrome coronavirus 2 0.008172931999999999 1 GCGGUAGUAGCAUGCUAGGGAGCAG template Severe acute respiratory syndrome coronavirus 2 0.008522079 1 UGACUGCUCCCUAGCAUGCUACUACCG ZINC ION 6.5409e-05 8 ZN PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER 0.000522196 1 GNP MAGNESIUM ION 2.4305e-05 1 MG water 1.8015e-05 1 HOH singleParticle particle 7.0 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD TUNGSTEN HAIRPIN 300 1.0 2.0 GATAN K2 QUANTUM (4k x 4k) 60.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.66 FSC 0.143 CUT-OFF 1351456 NOT APPLICABLE MAXIMUM LIKELIHOOD emd_34310.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 430.08 430.08 430.08 90.0 90.0 90.0 X Y Z -1.5466284 3.5371711 -0.0010453421 0.055557914 0.96 0.96 0.96 0.2 AUTHOR ::::EMDATABANK.org::::EMD-34310:::: emd_34310_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 430.08 430.08 430.08 90.0 90.0 90.0 X Y Z -0.69586307 1.9518518 0.0005403069 0.09073785 0.96 0.96 0.96 AUTHOR ::::EMDATABANK.org::::EMD-34310:::: emd_34310_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 448 448 448 0 0 0 448 448 448 430.08 430.08 430.08 90.0 90.0 90.0 X Y Z -0.6859172 2.0554118 0.0005502961 0.09072419 0.96 0.96 0.96 AUTHOR ::::EMDATABANK.org::::EMD-34310::::