Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position

2025-07-09 REL PDBe INITIAL_RELEASE REPOSITORY 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 chem_comp citation entity entity_poly entity_poly_seq ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_poly_seq_scheme pdbx_struct_assembly_gen pdbx_struct_conn_angle struct_asym struct_conn struct_ref_seq _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.group_PDB _atom_site.label_asym_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.type_symbol _chem_comp.name _chem_comp.pdbx_synonyms _citation.journal_volume _citation.year _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.seq_align_end DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _em_admin.last_update STRUCTURE_SUMMARY em_admin em_software pdbx_entry_details _em_admin.last_update _em_software.name _pdbx_entry_details.has_protein_modification PDBe PDBe 2022-10-20 2022-12-28 2022-12-28 2025-07-09 French National Research Agency France Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Cusack S Kouba T Influenza, viral RNA-dependent RNA polymerase; antiviral drug; nucleoside analogue; T705 (favipiravir); T1106; cap-dependent transcription; backtracking;, VIRAL PROTEIN Kouba T Dubankova A Drncova P Donati E Vidossich P Speranzini V Pflug A Huchting J Meier C De Vivo M Cusack S Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106. Cell Rep US 42 111901 111901 2023 36596301 doi:10.1016/j.celrep.2022.111901 2211-1247 8be0 FULLOVERLAP Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position Early transcription elongation state of influenza B/Mem polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the C +1 position 0 1 2 3 4 5 6 Influenza B virus (B/Memphis/13/2003) Polymerase acidic protein Influenza B virus (B/Memphis/13/2003) B/Memphis/13/2003 0.085822781 1 Trichoplusia ni LEVO GSHHHHHHHHGSGSMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLDEEGKAYTALEG QGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELM IFSYNQDYSLSNESSLDEEGKGRVLSRLTELQAELSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGM RSYIDNIDPKGAIERNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMSDELGLANMTEGKSKKPKTLA KECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNTISNEEMSNELQKTNYAKWATGDGLTYQKIMKEVAIDDETM CQEEPKIPNKCRVAAWVQTEMNLLSTLTSKRALDLPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLL NESNASMGKYKVIPITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDPRVDSGKWPKYTVFRIGSLFV SGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEAIVEQESSIQGYDMTKACFKGDRVNSPKTFSIGTQEGKLVK GSFGKALRVIFTKCLMHYVFGNAQLEGFSAESRRLLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEW LGFEKEGSKVLESVDEIMDEGSGSGENLYFQ Q5V8Z9 3.1.-.- RNA-directed RNA polymerase catalytic subunit Influenza B virus (B/Memphis/13/2003) B/Memphis/13/2003 0.086207016 1 Trichoplusia ni LEVO GSGSGSGSGMNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSNKGKQYISDVTGCTMVDPTNG PLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAMETLMVTTVDKLTQGRQTFDWTVCRNQPAATALNTTITSFR LNDLNGADKGGLIPFCQDIIDSLDRPEMTFFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDA ERGKLKRRAIATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLSNCPPGGISMTVTGDNTKWNE CLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARLGKGFMITSKTKRLKAQIPCPDLFSIPLERYNEETRAKLKK LKPFFNEEGTASLSPGMMMGMFNMLSTVLGVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKL LGINMSKKKSYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKNNMINNGMGPATAQTAIQLFI ADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVADGGPNIYNLRNLHIPEIVLKYNLMDPEYKGRLLHPQNPFV GHLSIEGIKEADITPAHGPVKKMDYDAVSGTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQH SMLEAMAHRLRMDARLDYESGRMSKDDFEKAMAHLGEIGYIGSGSGENLYFQ Q5V8Y6 2.7.7.48 Polymerase basic protein 2 Influenza B virus (B/Memphis/13/2003) B/Memphis/13/2003 0.09084410899999999 1 Trichoplusia ni LEVO GSGSGSGSGMTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKWAMCSNFPLALTKGDMANRIP LEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTEGFERVYESFFLRKMRLDNATWGRITFGPVERVRKRVLLNP LTKEMPPDEASNVIMEILFPKEAGIPRESTWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFI EMLHCLQGENWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVIDTEPLKSCLAAIDGGDVACD IIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNGTIQKIGIWDGEEEFHVRCGECRGILKKSKMKLEKLLINSA KKEDMRDLIILCMVFSQDTRMFQGVRGEINFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNA SDYTLKGVVVTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMITYDTPKMWEMGTTKELVQNTY QWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAGQYSGFARAVLKQMRDQEVMKTDQFIKLLPFCFSPPKLRSN GEPYQFLKLVLKGGGENFIEVRKGSPLFSYNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDF KTIEELEKLKPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSGWSHPQFEKGSGSENLYFQ Q5V8X3 5' vRNA Influenza B virus 0.00449574 1 AGUAGUAACAAGUU 3' vRNA Influenza B virus 0.006698029 1 UAUACAACUGACGAGGCUAUU mRNA Influenza B virus 0.006308756 1 AUCUAUAAUAGCCUC(K1F)UC(K1F)(K1F) MAGNESIUM ION 2.4305e-05 2 MG P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE 0.0007874409999999999 1 GTA water 1.8015e-05 95 HOH singleParticle particle 7.4 ETHANE FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.5 2.5 GATAN K3 BIOQUANTUM (6k x 4k) 40.0 1 PHASE FLIPPING ONLY 6T0V 2.34 FSC 0.143 CUT-OFF 302395 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_15996.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 270.9 270.9 270.9 90.0 90.0 90.0 X Y Z -0.2908768 0.93070394 0.0026803974 0.028314402 0.645 0.645 0.645 0.24 AUTHOR ::::EMDATABANK.org::::EMD-15996:::: Loc-Scale filtered emd_15996_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 270.9 270.9 270.9 90.0 90.0 90.0 X Y Z -0.035542667 0.069497906 0.000016749673 0.0027154302 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-15996:::: Relion post-processed emd_15996_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 270.9 270.9 270.9 90.0 90.0 90.0 X Y Z -0.008968798 0.024447838 0.00001686296 0.0008899893 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-15996:::: Half-map emd_15996_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 420 420 420 0 0 0 420 420 420 270.9 270.9 270.9 90.0 90.0 90.0 X Y Z -0.010089276 0.024579078 0.000016636373 0.000889531 0.645 0.645 0.645 AUTHOR ::::EMDATABANK.org::::EMD-15996:::: Half-map