2025-03-12 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_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_admin pdbx_entry_details _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 _pdbx_entry_details.has_protein_modification PDBe PDBe 2024-02-16 2024-06-12 2024-06-12 2025-03-12 German Research Foundation (DFG) WI3285/11-1 Germany Paternoga H Wilson DN Wilson DN LSU, 50S, RQC, YlmH, RIBOSOME, RqcH Takada H Paternoga H Fujiwara K Nakamoto JA Park EN Dimitrova-Paternoga L Beckert B Saarma M Tenson T Buskirk AR Atkinson GC Chiba S Wilson DN Hauryliuk V Nucleic Acids Res. UK 52 8483 8499 2024 38811035 doi:10.1093/nar/gkae399 1362-4962 0389 NARHAD EMD-19638 other EM volume

YlmH bound to the stalled 50S subunit

8s1u FULLOVERLAP 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH 50S ribosomal subunit with stalled P-tRNA-nascent chain, bound by YlmH 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 Bacillus subtilis subsp. subtilis str. 168 P-tRNA Bacillus subtilis subsp. subtilis str. 168 0.024491547 2 GGGGCCUUAGCUCAGCUGGGAGAGCGCCUGCUUUGCACGCAGGAGGUCAGCGGUUCGAUCCCGCUAGGCUCCACCA CP052842.1 50S ribosomal protein L32 Bacillus subtilis subsp. subtilis str. 168 0.006745073 1 LEVO MAVPFRRTSKMKKRLRRTHFKLNVPGMTECPSCGEMKLSHRVCKACGSYNGKDINVKSN O34687 50S ribosomal protein L33 1 Bacillus subtilis subsp. subtilis str. 168 0.005915875 1 LEVO MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK P56849 50S ribosomal protein L34 Bacillus subtilis subsp. subtilis str. 168 0.005271332 1 LEVO MKRTFQPNNRKRSKVHGFRSRMSSKNGRLVLARRRRKGRKVLSA P05647 50S ribosomal protein L35 Bacillus subtilis subsp. subtilis str. 168 0.0075811279999999995 1 LEVO MPKMKTHRGSAKRFKKTGSGKLKRSHAYTSHLFANKSQKQKRKLRKSAVVSAGDFKRIKQMLANIK P55874 50S ribosomal protein L36 Bacillus subtilis subsp. subtilis str. 168 0.004318422 1 LEVO MKVRPSVKPICEKCKVIRRKGKVMVICENPKHKQKQG P20278 50S ribosomal protein L31 Bacillus subtilis subsp. subtilis str. 168 0.007458582 1 LEVO MKAGIHPNFKKATVKCACGNEFETGSVKEEVRVEICSECHPFYTGRQKFASADGRVDRFNKKYGLK Q03223 5S rRNA Bacillus subtilis subsp. subtilis str. 168 0.03615752 1 UGGUGGCGAUAGCGAAGAGGUCACACCCGUUCCCAUACCGAACACGGAAGUUAAGCUCUUCAGCGCCGAUGGUAGUCGGG GGUUUCCCCCUGUGAGAGUAGGACGCCGCCAA CP019662.1 50S ribosomal protein L2 Bacillus subtilis subsp. subtilis str. 168 0.030335124999999998 1 LEVO MAIKKYKPTSNGRRGMTTSDFAEITTDKPEKSLLAPLHKKGGRNNQGKLTVRHQGGGHKRQYRVIDFKRDKDGIPGRVAT VEYDPNRSANIALINYADGEKRYILAPKGIQVGTEIMSGPEADIKVGNALPLINIPVGTVVHNIELKPGKGGQLVRSAGT SAQVLGKEGKYVLVRLNSGEVRMILSACRASIGQVGNEQHELINIGKAGRSRWKGIRPTVRGSVMNPNDHPHGGGEGRAP IGRKSPMSPWGKPTLGFKTRKKKNKSDKFIVRRRKNK P42919 50S ribosomal protein L3 Bacillus subtilis subsp. subtilis str. 168 0.022723348 1 LEVO MTKGILGRKIGMTQVFAENGDLIPVTVIEAAPNVVLQKKTAENDGYEAIQLGFDDKREKLSNKPEKGHVAKAETAPKRFV KELRGVEMDAYEVGQEVKVEIFSAGEIVDVTGVSKGKGFQGAIKRHGQSRGPMSHGSRYHRRPGSMGPVDPNRVFKGKLL PGRMGGEQITVQNLEIVKVDAERNLLLIKGNVPGAKKSLITVKSAVKSK P42920 50S ribosomal protein L4 Bacillus subtilis subsp. subtilis str. 168 0.022424951 1 LEVO MPKVALYNQNGSTAGDIELNASVFGIEPNESVVFDAILMQRASLRQGTHKVKNRSEVRGGGRKPWRQKGTGRARQGSIRS PQWRGGGVVFGPTPRSYSYKLPKKVRRLAIKSVLSSKVIDNNIIVLEDLTLDTAKTKEMAAILKGLSVEKKALIVTADAN EAVALSARNIPGVTVVEANGINVLDVVNHEKLLITKAAVEKVEEVLA P42921 50S ribosomal protein L5 Bacillus subtilis subsp. subtilis str. 168 0.020177564 1 LEVO MNRLKEKYNKEIAPALMTKFNYDSVMQVPKIEKIVINMGVGDAVQNAKAIDSAVEELTFIAGQKPVVTRAKKSIAGFRLR EGMPIGAKVTLRGERMYDFLDKLISVSLPRVRDFRGVSKKSFDGRGNYTLGIKEQLIFPEIDYDKVTKVRGMDIVIVTTA NTDEEARELLTQVGMPFQK P12877 Large ribosomal subunit protein uL6 Bacillus subtilis subsp. subtilis str. 168 0.019543388999999998 1 LEVO MSRVGKKLLEIPSDVTVTLNDNNTVAVKGPKGELTRTFHPDMEIKVEDNVLTVARPSDQKEHRALHGTTRSLLGNMVEGV SKGFERGLELVGVGYRASKSGNKLVLNVGYSHPVEIVPEEGIEIEVPSQTKVVVKGTDKERVGAIAANIRAVRSPEPYKG KGIRYEGEVVRRKEGKSAK P46898 50S ribosomal protein L13 Bacillus subtilis subsp. subtilis str. 168 0.016407104 1 LEVO MRTTPMANASTIERKWLVVDAAGKTLGRLSSEVAAILRGKHKPTYTPHVDTGDHVIIINAEKIELTGKKLTDKIYYRHTQ HPGGLKSRTALEMRTNYPEKMLELAIKGMLPKGSLGRQMFKKLNVYRGSEHPHEAQKPEVYELRG P70974 50S ribosomal protein L14 Bacillus subtilis subsp. subtilis str. 168 0.013175288 1 LEVO MIQQETRLKVADNSGAREVLTIKVLGGSGRKTANIGDVIVCTVKQATPGGVVKKGEVVKAVIVRTKSGARRSDGSYISFD ENACVIIRDDKSPRGTRIFGPVARELRENNFMKIVSLAPEVI P12875 50S ribosomal protein L15 Bacillus subtilis subsp. subtilis str. 168 0.015410693999999999 1 LEVO MKLHELKPSEGSRKTRNRVGRGIGSGNGKTAGKGHKGQNARSGGGVRPGFEGGQMPLFQRLPKRGFTNINRKEYAVVNLD KLNGFAEGTEVTPELLLETGVISKLNAGVKILGNGKLEKKLTVKANKFSASAKEAVEAAGGTAEVI P19946 50S ribosomal protein L16 Bacillus subtilis subsp. subtilis str. 168 0.016223049 1 LEVO MLLPKRVKYRREHRGKMRGRAKGGTEVHFGEFGIQALEASWITNRQIEAARIAMTRYMKRGGKVWIKIFPSKPYTAKPLE VRMGSGKGAPEGWVAVVKPGKVLFEISGVSEEVAREALRLASHKLPIKTKFVKREEIGGESNES P14577 50S ribosomal protein L17 Bacillus subtilis subsp. subtilis str. 168 0.013774806 1 LEVO MSYRKLGRTSAQRKAMLRDLTTDLIINERIETTETRAKELRSVVEKMITLGKRGDLHARRQAAAYIRNEVANEENNQDAL QKLFSDIATRYEERQGGYTRIMKLGPRRGDGAPMAIIELV P20277 50S ribosomal protein L18 Bacillus subtilis subsp. subtilis str. 168 0.012993828999999998 1 LEVO MITKTSKNAARLKRHARVRAKLSGTAERPRLNVFRSNKHIYAQIIDDVNGVTLASASTLDKDLNVESTGDTSAATKVGEL VAKRAAEKGISDVVFDRGGYLYHGRVKALADAAREAGLKF P46899 50S ribosomal protein L19 Bacillus subtilis subsp. subtilis str. 168 0.013416852999999998 1 LEVO MQKLIEDITKEQLRTDLPAFRPGDTLRVHVKVVEGNRERIQIFEGVVIKRRGGGISETFTVRKISYGVGVERTFPVHTPK IAKIEVVRYGKVRRAKLYYLRELRGKAARIKEIRR O31742 Large ribosomal subunit protein bL20 Bacillus subtilis subsp. subtilis str. 168 0.013669189 1 LEVO MPRVKGGTVTRKRRKKVLKLAKGYFGSKHTLYKVANQQVMKSGNYAFRDRRQKKRDFRKLWITRINAAARMNGLSYSRLM HGLKLSGIEVNRKMLADLAVNDLTAFNQLADAAKAQLNK P55873 50S ribosomal protein L21 Bacillus subtilis subsp. subtilis str. 168 0.011296081 1 LEVO MYAIIKTGGKQIKVEEGQTVYIEKLAAEAGETVTFEDVLFVGGDNVKVGNPTVEGATVTAKVEKQGRAKKITVFRYKPKK NVHKKQGHRQPYTKVTIEKINA P26908 50S ribosomal protein L22 Bacillus subtilis subsp. subtilis str. 168 0.012481608 1 LEVO MQAKAVARTVRIAPRKARLVMDLIRGKQVGEAVSILNLTPRAASPIIEKVLKSAIANAEHNYEMDANNLVISQAFVDEGP TLKRFRPRAMGRASQINKRTSHITIVVSEKKEG P42060 Large ribosomal subunit protein uL23 Bacillus subtilis subsp. subtilis str. 168 0.010978813 1 LEVO MKDPRDVLKRPVITERSADLMTEKKYTFEVDVRANKTEVKDAVESIFGVKVDKVNIMNYKGKSKRVGRYTGMTSRRRKAI VKLTADSKEIEIFEA P42924 50S ribosomal protein L24 Bacillus subtilis subsp. subtilis str. 168 0.01116612 1 LEVO MHVKKGDKVMVISGKDKGKQGTILAAFPKKDRVLVEGVNMVKKHSKPTQANPQGGISNQEAPIHVSNVMPLDPKTGEVTR VGYKVEDGKKVRVAKKSGQVLDK P0CI78 Putative RNA-binding protein YlmH Bacillus subtilis subsp. subtilis str. 168 0.030823839999999998 1 Bacillus subtilis LEVO MSDIYQHFRKDERAFIDQALEWKRIVQEQYRMKLTDFLDPREQVILSAVTGQADVGLAFSGGYDRAERKRAILFPEYITP EESDFELQAFNVRYADKFVSVDHRSLLGALMGIGLKRQKFGDIVFSETAVQLIVSADTADFVAAQLTQAGKAAVSLEKID LSDLNIPAVDVEIRDDTVSSLRLDAVCASMSRQSRQKSQTLVKNGLVKVNWKVVEDPSYIVAEGDMLSIRGFGRCSLTKI EGKTKKDKWRVTFERQKGSGSGSGSGSDYKDDDDK P71020 Large ribosomal subunit protein bL27 Bacillus subtilis subsp. subtilis str. 168 0.010391854999999998 1 LEVO MLRLDLQFFASKKGVGSTKNGRDSEAKRLGAKRADGQFVTGGSILYRQRGTKIYPGENVGRGGDDTLFAKIDGTVKFERF GRDRKKVSVYPVAQ P05657 50S ribosomal protein L28 Bacillus subtilis subsp. subtilis str. 168 0.006826144 1 LEVO MARKCVITGKKTTAGNNRSHAMNASKRTWGANLQKVRILVNGKPKKVYVSARALKSGKVERV P37807 50S ribosomal protein L29 Bacillus subtilis subsp. subtilis str. 168 0.007728029 1 LEVO MKANEIRDLTTAEIEQKVKSLKEELFNLRFQLATGQLENTARIREVRKAIARMKTVIREREIAANK P12873 Large ribosomal subunit protein uL30 Bacillus subtilis subsp. subtilis str. 168 0.006650795 1 LEVO MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ P19947 Rqc2 homolog RqcH Bacillus subtilis subsp. subtilis str. 168 0.065307398 1 LEVO MSFDGMFTYGMTHELNEKIMGGRITKIHQPYKHDVIFHIRAKGKNQKLLLSAHPSYSRVHITAQAYENPSEPPMFCMLLR KHIEGGFIEKIEQAGLDRIMIFHIKSRNEIGDETVRKLYVEIMGRHSNIILTDAAENVIIDGLKHLSPSMNSYRTVLPGQ DYKLPPAQDKISPLEASEDDILRHLSFQEGRLDKQIVDHFSGVSPLFAKEAVHRAGLANKVTLPKALLALFAEVKEHRFI PNITTVNGKEYFYLLELTHLKGEARRFDSLSELLDRFYFGKAERDRVKQQAQDLERFVVNERKKNANKIKKLEKTLEYSE NAKEFQLYGELLTANLYMLKKGDKQAEVINYYDEESPTITIPLNPNKTPSENAQAYFTKYQKAKNSVAVVEEQIRLAQEE IEYFDQLIQQLSSASPRDISEIREELVEGKYLRPKQQKGQKKQKPHNPVLETYESTSGLTILVGKNNRQNEYLTTRVAAR DDIWLHTKDIPGSHVVIRSSEPDEQTIMEAATIAAYFSKAKDSSSVPVDYTKIRHVKKPNGAKPGFVTYDSQHTVFVTPD ADTVIKLKKS O34693 23S rRNA Bacillus subtilis subsp. subtilis str. 168 0.9497613749999999 1 GGUUAAGUUAGAAAGGGCGCACGGUGGAUGCCUUGGCACUAGGAGCCGAUGAAGGACGGGACGAACACCGAUAUGCUUCG GGGAGCUGUAAGCAAGCUUUGAUCCGGAGAUUUCCGAAUGGGGAAACCCACCACUCGUAAUGGAGUGGUAUCCAUAUCUG AAUUCAUAGGAUAUGAGAAGGCAGACCCGGGGAACUGAAACAUCUAAGUACCCGGAGGAAGAGAAAGCAAAUGCGAUUCC CUGAGUAGCGGCGAGCGAAACGGGAUCAGCCCAAACCAAGAGGCUUGCCUCUUGGGGUUGUAGGACACUCUGUACGGAGU UACAAAGGAACGAGGUAGAUGAAGAGGUCUGGAAAGGCCCGCCAUAGGAGGUAACAGCCCUGUAGUCAAAACUUCGUUCU CUCCUGAGUGGAUCCUGAGUACGGCGGAACACGUGAAAUUCCGUCGGAAUCCGGGAGGACCAUCUCCCAAGGCUAAAUAC UCCCUAGUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGUGAAAAGCACCCCGGAAGGGGAGUGAAAGAGAUCCUGAA ACCGUGUGCCUACAAGUAGUCAGAGCCCGUUAACGGGUGAUGGCGUGCCUUUUGUAGAA(5MU)GAACCGGCGAGUUACG AUCUCGUGCAAGGUUAAGCAGAAGAUGCGGAGCCGCAGCGAAAGCGAGUCUGAAUAGGGCGCAUGAGUACGUGGUCGUAG ACCCGAAACCAGGUGAUCUACCCAUGUCCAGGGUGAAGUUCAGGUAACACUGAAUGGAGGCCCGAACCCACGCACGU (5MU)GAAAAGUGCGGGGAUGAGGUGUGGGUAGGGGUGAAAUGCCAAUCGAACCUGGAGAUAGCUGGUUCUCUCCGAAAU AGCUUUAGGGCUAGCCUCAAGGUAAGAGUCUUGGAGGUAGAGCACUGAUUGGACUAGGGGCCCCUACCGGGUUACCGAAU UCAGUCAAACUCCGAAUGCCAAUGACUUAUCCUUGGGAGUCAGACUGCGAG(PSU)GAUAAGAUCCGUAGUCGAAAGGGA AACAGCCCAGACCGCCAGCUAAGGUCCCAAAGUAUACGUUAAGUGGAAAAGGAUGUGGAGUUGCUUAGACAACCAGGAUG UUGGCUUAGAAGCAGCCACCAUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACUCUGCGCCGAAAAUGUACCGGGG CUAAACGUAUCACCGAAGCUGCGGACUGUUCUUCGAACAGUGGUAGGAGAGCGUUCUAAGGGCUGUGAAGCCAGACCGGA AGGACUGGUGGAGCGCUUAGAAGUGAGAAUGCCGGUAUGAGUAGCGAAAGAGGGGUGAGAAUCCCCUCCACCGAAUGCCU AAGGUUUCCUGAGGAAGGCUCGUCCGCUCAGGGUUAGUCGGGACCUAAGCCGAGGCCGAAAGGCGUAGGCGAUGGACAAC AGGUUGAUAUUCCUGUACCACCUCCUCACCAUUUGAGCAAUGGGGGGACGCAGGAGGAUAGGGUAAGCGCGGUAUUGGAU AUCCGCGUCCAAGCAGUUAGGCUGGGAAAUAGGCAAAUCCGUUUCCCAUAAGGCUGAGCUGUGAUGGCGAGCGAAAUAUA GUAGCGAAGUUCCUGAUUCCACACUGCCAAGAAAAGCCUCUAGCGAGGUGAGAGGUGCCCGUACCGCAAACCGACACAGG UAGGCGAGGAGAGAAUCCUAAGGUGAUCGAGAGAACUCUCGUUAAGGAACUCGGCAAAAUGACCCCGUAACUUCGGGAGA AGGGGUGCUCUGUUAGGGUGCAAGCCCGAGAGAGCCGCAGUGAAUAGGCCCAGGCGACUGUUUAGCAAAAACACAGGUCU CUGCGAAGCCGUAAGGCGAAGUAUAGGGGCUGACGCCUGCCCGGUGCUGGAAGGUUAAGAGGAGCGCUUAGCGUAAGCGA AGGUGCGAAUUGAAGCCCCAGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUA AGUUCCGACCCGCACGAAAGGCGCAACGAUCUGGGCACUGUCUCAACGAGAGACUCGGUGAAAUUAUAGUACCUGUGAAG AUGCAGGUUACCCGCGACAGGACGGAAAGACCCCGUGGAGCUUUACUGCAGCCUGAUAUUGAAUGUUGGUACAGCUUGUA CAGGAUAGGUAGGAGCCUUGGAAACCGGAGCGCCAGCUUCGGUGGAGGCAUCGGUGGGAUACUACCCUGGCUGUAUUGAC CUUCUAACCCGCCGCCCUUAUCGGGCGGGGAGACAGUGUCAGGUGGGCAGUUUGACUG(OMG)GGCGGUCGCCUCCUAAA AGGUAACGGAGGCGCCCAAAGGUUCCCUCAGAAUGGUUGGAAAUCAUUCGCAGAGUGUAAAGGCACAAGGGAGCUUGACU GCGAGACCUACAAGUCGAGCAGGGACGAAAGUCGGGCUUAGUGAUCCGGUGGUUCCGCAUGGAAGGGCCAUCGCUCAACG GAUAAAAGCUACCCCG(2MG)GGA(H2U)AACAGGC(PSU)UAUCUCCCCCAAGAGUCCACAUCGACGGGGAGGUUUGGC ACCUCG(2MA)(PSU)GUCGGCUCAUCGCAUCCUGGGGCUGUAGUCGGUCCCAAGGGUUGGGCU(OMG)UUCGCCCAUUA AAGCGGUAC(G7M)CGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGUCGCGGGCGCAGGAAAUUUGAG AGGAGCUGUCCUUAGUACGAGAGGACCGGGAUGGACGCACCGCUGGUGUACCAGUUGUUCUGCCAAGGGCAUCGCUGGGU AGCUAUGUGCGGACGGGAUAAGUGCUGAAAGCAUCUAAGCAUGAAGCCCCCCUCAAGAUGAGAUUUCCCAUUCCGCAAGG AAGUAAGAUCCCUGAAAGAUGAUCAGGUUGAUAGGUCUGAGGUGGAAGUGUGGCGACACAUGGAGCUGACAGAUACUAAU CGAUCGAGGACUUAACCAU POTASSIUM ION 3.9098e-05 15 K singleParticle particle 7.5 Quantifoil R3/3 COPPER 300 CARBON CONTINUOUS 3.0 ETHANE-PROPANE 100 FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 0.9 FEI FALCON IV (4k x 4k) 40.0 1 2550984 6HA8

Bacillus subtilis 70S

3.4 FSC 0.143 CUT-OFF RELION 4.0.1 3770 MAXIMUM LIKELIHOOD RELION 4.0.1 MAXIMUM LIKELIHOOD RELION 4.0.1 emd_19641_msk_1.map emd_19641_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 307.2 307.2 307.2 90.0 90.0 90.0 X Y Z -0.015788088 0.032479443 0.000077629134 0.0024203015 0.8 0.8 0.8 AUTHOR ::::EMDATABANK.org::::EMD-19641:::: emd_19641_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 307.2 307.2 307.2 90.0 90.0 90.0 X Y Z -0.12098574 0.13267921 0.00007724973 0.015933381 0.8 0.8 0.8 AUTHOR ::::EMDATABANK.org::::EMD-19641:::: emd_19641_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 384 384 384 0 0 0 384 384 384 307.2 307.2 307.2 90.0 90.0 90.0 X Y Z -0.13713777 0.13495456 0.0000783472 0.016071908 0.8 0.8 0.8 AUTHOR ::::EMDATABANK.org::::EMD-19641::::