2026-04-01 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DERIVED_CALCULATIONS atom_site chem_comp chem_comp_atom chem_comp_bond database_PDB_caveat em_admin ndb_struct_na_base_pair ndb_struct_na_base_pair_step pdbx_struct_conn_angle struct_conn _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.label_atom_id _chem_comp.mon_nstd_flag _chem_comp.type _chem_comp_atom.atom_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _em_admin.last_update _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.hbond_type_12 _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_name _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.inclination _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_comp_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.step_name _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_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_atom_id EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update PDBe PDBe 2025-10-21 2026-03-18 2026-03-18 2026-04-01 Swedish Research Council 2016-06264 Sweden Swedish Research Council 2017-03827 Sweden Swedish Research Council 2022-04511 Sweden Larsson DSD Selmer M RNA modifications, ribosome biogenesis, maturation, RIBOSOME Larsson DSD Liiv A Ero R Remme J Selmer M Biorxiv US 2026 doi:10.64898/2026.03.01.708810 2692-8205 9t1b FULLOVERLAP EMDB EMD-55429 associated EM volume

E. coli 70S ribosome from delta-RlmE strain, PTC class 2

70S ribosome 70S ribosome 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 Escherichia coli 2.5 tRNA(Phe) Escherichia coli 0.024751018 1 GCCCGGA(4SU)AGCUCAG(H2U)CGG(H2U)AGAGCAGGGGA(PSU)UGAA(MIA)A(PSU)CCCCGU(7MG)(3AU)C CUUGG(5MU)(PSU)CGAUUCCGAGUCCGGGCACCA CP054236.1 tRNA(fMet) Escherichia coli 0.024848918 1 CGCGGGG(4SU)GGAGCAGCCUGG(H2U)AGCUCGUCGGG(OMC)UCAUAACCCGAAGGUCGUCGG(5MU)(PSU)CAAA UCCGGCCCCCGCAACCA CP053605.1 23S rRNA Escherichia coli 0.941813562 1 GGUUAAGCGACUAAGCGUACACGGUGGAUGCCCUGGCAGUCAGAGGCGAUGAAGGACGUGCUAAUCUGCGAUAAGCGUCG GUAAGGUGAUAUGAACCGUUAUAACCGGCGAUUUCCGAAUGGGGAAACCCAGUGUGUUUCGACACACUAUCAUUAACUGA AUCCAUAGGUUAAUGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCCCC AGUAGCGGCGAGCGAACGGGGAGCAGCCCAGAGCCUGAAUCAGUGUGUGUGUUAGUGGAAGCGUCUGGAAAGGCGCGCGA UACAGGGUGACAGCCCCGUACACAAAAAUGCACAUGCUGUGAGCUCGAUGAGUAGGGCGGGACACGUGGUAUCCUGUCUG AAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUCCUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAA GAACCCCGGCGAGGGGAGUGAAAAAGAACCUGAAACCGUGUACGUACAAGCAGUGGGAGCACGCUUAGGCGUGUGACUGC GUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCUGUAGCAAGGUUAACCGAAUAGGGGAGCCGAAGGGAAACCGAGUC UUAACUGGGCGUUAAGUUGCAGGGUAUAGACCCGAAACCCGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGGGUAACACU AACUGGAGGACCGAACCGACUAAU(1MG)(PSU)(5MU)GAAAAAUUAGCGGAUGACUUGUGGCUGGGGGUGAAAGGCCA AUCAAACCGGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGUGAAUUCAUCUCCGGGGGUAGAGCACU GUUUCGGCAAGGGGGUCAUCCCGACUUACCAACCCGAUGCAAACUGCGAAUACCGGAGAAUGUUAUCACGGGAGACACAC 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)UGCACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUG(6MZ)AG AUGCAGUGUACCCGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGA UGUGUAGGAUAGGUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUU UGAUGUUCUAACGUUGACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCC UAAAGAGUAACGGAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUU GACUGCGAGCGUGACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUC AACGGAUAAAAGGUACUCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUU UGGCA(OMC)CU(TKW)G(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGCUGUUC GCCAUUUAAAGUGGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAG(PSU)(PSU)CGGUCCCUAUCUGCCGUGG GCGCUGGAGAACUGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCC AAUGGCACUGCCCGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUU CUCCCUGACCCUUUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCG UUGAGCUAACCGGUACUAAUGAACCGUGAGGCUUAACCUU 5S rRNA Escherichia coli 0.03879008999999999 1 UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU CP035706.1 Large ribosomal subunit protein uL2 Escherichia coli 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 Large ribosomal subunit protein uL3 Escherichia coli 0.022291562 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 Large ribosomal subunit protein uL4 Escherichia coli 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA P60723 Large ribosomal subunit protein uL13 Escherichia coli 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI P0AA10 Large ribosomal subunit protein uL15 Escherichia coli 0.015008470999999999 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE P02413 Large ribosomal subunit protein uL16 Escherichia coli 0.015343326999999999 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV (4D4)(MS6)GKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM A7ZSK2 Large ribosomal subunit protein bL21 Escherichia coli 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA P0AG48 Large ribosomal subunit protein uL22 Escherichia coli 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR P61175 Large ribosomal subunit protein bL27 Escherichia coli 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 Large ribosomal subunit protein bL32 Escherichia coli 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK P0A7N4 N~1~-(3-azaniumylpropyl)butane-1,4-diaminium 0.00014827000000000002 2 SR0 1,4-DIAMINOBUTANE 8.815099999999999e-05 1 PUT MAGNESIUM ION 2.4305e-05 102 MG POTASSIUM ION 3.9098e-05 43 K singleParticle particle 7.5 5.0 C8H18N2O4S HEPES 5.0 Mg(OAc)2 magnesium acetate 5.0 NH4Cl ammonium chloride 5.0 CaCl2 calcium chloride 100.0 KCl potassium chloride 1.0 C7H19N3 spermidine 8.0 C4H12N2 putrescine 5.0 C2H6OS 2-mercaptoethanol

HEPES-polymix buffer (pH-7.5)

Quantifoil R2/2 COPPER 300 CARBON HOLEY CARBON CONTINUOUS 2.0 GLOW DISCHARGE 20 AIR 0.04 ETHANE 277 FEI VITROBOT MARK IV TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.7000000000000001 1.5 GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) COUNTING 1 10424 2.1 42.1 1 736925 cryoSPARC 4.4 PHASE FLIPPING AND AMPLITUDE CORRECTION 1 FOURIER SPACE 2.32 FSC 0.143 CUT-OFF cryoSPARC 4.4 53040 MAXIMUM LIKELIHOOD cryoSPARC MAXIMUM LIKELIHOOD cryoSPARC 4.4 10 cryoSPARC 4.4 9SYH PDB experimental model FLEXIBLE FIT REAL 27.350000000000001 emd_55429_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 421.2736 421.2736 421.2736 90.0 90.0 90.0 X Y Z -0.40624022 0.713882 0.0013956104 0.054272257 0.8228 0.8228 0.8228 AUTHOR ::::EMDATABANK.org::::EMD-55429:::: emd_55429_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 512 512 512 0 0 0 512 512 512 421.2736 421.2736 421.2736 90.0 90.0 90.0 X Y Z -0.40618554 0.6952969 0.0013948312 0.054370362 0.8228 0.8228 0.8228 AUTHOR ::::EMDATABANK.org::::EMD-55429::::