Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region)

2026-09-23 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update POLYMER_SEQUENCE entity_poly pdbx_audit_support _entity_poly.pdbx_seq_one_letter_code_can _pdbx_audit_support.funding_organization STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond database_2 em_admin pdbx_entry_details pdbx_modification_feature pdbx_struct_conn_angle struct_conn struct_conn_type _database_2.pdbx_DOI _database_2.pdbx_database_accession _em_admin.last_update _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.value _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_asym_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_conn_type.id DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _chem_comp_atom.atom_id _chem_comp_atom.pdbx_aromatic_flag _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update DATA_COLLECTION em_admin _em_admin.last_update EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update RCSB RCSB 2018-01-12 2018-02-21 2018-02-21 2026-09-23 National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01-GM120552 United States Conformation of methylated GGQ in the peptidyl transferase center during translation termination (PTC region) Zeng F Jin H nonstop, termination, ArfA, RF2, methylation, RIBOSOMAL PROTEIN-RNA complex Zeng F Jin H Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination. Sci Rep UK 8 2349 2349 2018 29403017 doi:10.1038/s41598-018-20107-8 2045-2322 EMD-7341 other EM volume 6c4h FULLOVERLAP EMDB EMD-7340 associated EM volume

Conformation of methylated GGQ in the peptidyl transferase center during translation termination

EMDB EMD-7341 other EM volume nonstop ribosomal complex with ArfA/RF2 nonstop ribosomal complex with ArfA/RF2 0 1 2 3 4 5 6 7

nonstop termination complex with 70S, ArfA, RF2, tRNA and nonstop mRNA

50S subunit 1 1 2 3 4 5 Escherichia coli P-site tRNA fMet 1 6 Escherichia coli Peptide chain release factor 2 1 7 Escherichia coli 23S rRNA 2 1 Escherichia coli 50S ribosomal protein L2 2 2 Escherichia coli 50S ribosomal protein L3 2 3 Escherichia coli 50S ribosomal protein L16 2 4 Escherichia coli 50S ribosomal protein L27 2 5 Escherichia coli 23S rRNA Escherichia coli 0.9418186249999999 1 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU GUUUCGGCAAGGGGGUCAACCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACAC GGCGGG(PSU)GCUAACGUCCGUCGUGAAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAGUCAUGGUUAAGUG GGAAACGAUGUGGGAAGGCCCAGACAGCCAGGAUGUUGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCAC UGGUCGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAACCAUGCACCGAAGCUGCGGCAGCGACGCUUAUGCGUUGUU GGGUAGGGGAGCGUUCUGUAAGCCUGCGAAGGUGUGCUGUGAGGCAUGCUGGAGGUAUCAGAAGUGCGAAUGCUGACAUA AGUAACGAUAAAGCGGGUGAAAAGCCCGCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUGAGU CGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACAGGUUAAUAUUCCUGUACUUGGUGUUACUGCGAAGGGG GGACGGAGAAGGCUAUGUUGGCCGGGCGACGGUUGUCCCGGUUUAAGCGUGUAGGCUGGUUUUCCAGGCAAAUCCGGAAA AUCAAGGCUGAGGCGUGAUGACGAGGCACUACGGUGCUGAAGCAACAAAUGCCCUGCUUCCAGGAAAAGCCUCUAAGCAU CAGGUAACAUCAAAUCGUACCCCAAACCGACAC(6MZ)GGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGG GUGAAGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAG CUGAAAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAU ACGGUGUGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCG GUAAACGGCGGCCG(PSU)AAC(3TD)A(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGA C(5MC)UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGC AGUGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUG UAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAU GUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCCUAAA GAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACU GCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACG GAUAAAAGGUACUCCG(2MG)GGAUAACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCA (OMC)CUCG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUCGCCAU UUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAGU(PSU)CGGUCCCUAUCUGCCGUGGGCGCUGGAG AACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACU GCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGAC CCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAA CCGGUACUAAUGAACCGUGAGGCUUAACCUU LM993812.1 50S ribosomal protein L2 Escherichia coli 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 50S ribosomal protein L3 Escherichia coli 0.022277534999999998 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKK MAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 50S ribosomal protein L16 Escherichia coli 0.015312269 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV RMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM P0ADY7 50S ribosomal protein L27 Escherichia coli 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 P-site tRNA fMet Escherichia coli 0.024786785 1 CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGAUCGUCGGUUCAAAUCCGGCCCCCGCAACCA CP011320.1 Peptide chain release factor RF2 Escherichia coli 0.043384945 1 Escherichia coli LEVO AHHHHHHSAALEVLFQGPGMFEINPVNNRIQDLTERSDVLRGYLDYDAKKERLEEVNAELEQPDVWNEPERAQALGKERS SLEAVVDTLDQMKQGLEDVSGLLELAVEADDEETFNEAVAELDALEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEA QDWASMLERMYLRWAESRGFKTEIIEESEGEVAGIKSVTIKISGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAF VYPEVDDDIDIEINPADLRIDVYRTSGAGG(MEQ)HVNRTESAVRITHIPTGIVTQCQNDRSQHKNKDQAMKQMKAKLYE LEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL P07012 MAGNESIUM ION 2.4305e-05 34 MG singleParticle particle 7.5 20.0 C8H18N2O4S 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 15.0 Mg(CH3COO)2 magnesium acetate 150.0 CH3CO2K potassium acetate 4.0 HOCH2CH2SH beta-mercapthoethanol 2.0 C7H19N3 spermidine 0.05 C10H26N4 spermine C-flat-2/0.5 4C GLOW DISCHARGE ETHANE 100 277 FEI VITROBOT MARK IV

Grids were blotted for 3.5 seconds..

JEOL 3200FS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 83822.0 NITROGEN GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 20.0 1 CTFFIND 4 PHASE FLIPPING AND AMPLITUDE CORRECTION EMD-8505 1 C1 3.1 FSC 0.143 CUT-OFF RELION 2 143372 ANGULAR RECONSTITUTION RELION 2 ANGULAR RECONSTITUTION RELION 2 RELION 2 emd_7340.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 460.80002 460.80002 460.80002 90.0 90.0 90.0 X Y Z -0.2639116 0.39169636 0.00007359937 0.011791689 1.2 1.2 1.2 0.04 AUTHOR ::::EMDATABANK.org::::EMD-7340:::: Conformation of methylated GGQ in the peptidyl transferase center during translation termination FLEXIBLE FIT Average FSC RECIPROCAL