2025-03-12 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY REFINEMENT_DESCRIPTION em_3d_fitting_list em_admin _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update STRUCTURE_SUMMARY chem_comp_atom chem_comp_bond em_3d_fitting_list em_admin pdbx_entry_details pdbx_modification_feature struct_conn _em_3d_fitting_list.accession_code _em_3d_fitting_list.initial_refinement_model_id _em_3d_fitting_list.source_name _em_3d_fitting_list.type _em_admin.last_update _pdbx_entry_details.has_protein_modification _struct_conn.pdbx_leaving_atom_flag PDBe PDBe 2022-01-06 2023-01-18 2023-01-18 2025-03-12 German Research Foundation (DFG) WI3285/6-1 Germany Koller TO Beckert B Wilson DN Ribosome, Antibiotic, Myxovalargin A, MyxA Koller TO Scheid U Kosel T Herrmann J Krug D Boshoff HIM Beckert B Evans JC Schlemmer J Sloan B Weiner DM Via LE Moosa A Ioerger TR Graf M Zinshteyn B Abdelshahid M Nguyen F Arenz S Gille F Siebke M Seedorf T Plettenburg O Green R Warnke AL Ullrich J Warrass R Barry 3rd CE Warner DF Mizrahi V Kirschning A Wilson DN Muller R J.Am.Chem.Soc. US 145 851 863 2023 36603206 doi:10.1021/jacs.2c08816 1520-5126 JACSAT 7qq3 FULLOVERLAP Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. Cryo-EM structure of the E.coli 50S ribosomal subunit in complex with the antibiotic Myxovalargin A. 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 Escherichia coli K-12 MG1650 1.356 23S ribosomal RNA Escherichia coli K-12 0.941752562 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 CAGGUAACAUCAAAUCGUACCCCAAACCGACACAGGUGGUCAGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGA AGGAACUAGGCAAAAUGGUGCCGUAACUUCGGGAGAAGGCACGCUGAUAUGUAGGUGAGGUCCCUCGCGGAUGGAGCUGA AAUCAGUCGAAGAUACCAGCUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAACACGAAAGUGGACGUAUACGG UGUGACGCCU(2MG)CCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGCGCAAGCGAAGCUCUUGAUCGAAGCCCCGGUAA ACGGCGGCCG(PSU)AACUA(PSU)AACGGUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGGUAAGUUCCGAC(5MC)UG CACGAAUGGCGUAAUGAUGGCCAGGCUGUCUCCACCCGAGACUCAGUGAAAUUGAACUCGCUGUGAAGAUGCAGUGUACC CGCGGCAAGACGGAAAGACCCCGUGAACCUUUACUAUAGCUUGACACUGAACAUUGAGCCUUGAUGUGUAGGAUAGGUGG GAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAACGUUG ACCCGUAAUCCGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCCUAAAGAGUAACGGAGG AGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGUGACG GCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUAC UCCG(2MG)GGAUAACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCA(OMC)CUCG(2MA) (PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUCGCCAUUUAAAGUGGUACGC GAGC(PSU)GGGUUUAGAACGUCGUGAGACAGU(PSU)CGGUCCCUAUCUGCCGUGGGCGCUGGAGAACUGAGGGGGGCU GCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCCCGGUAGCUAAA UGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCUUUAAGGGUCCU GAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCGGUACUAAUGAA CCGUGAGGCUUAACCUU CP011343.2 5S ribosomal RNA Escherichia coli K-12 0.038815098 1 UGCCUGGCGGCAGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCUCAUGCGAGAGUAGGGAACUGCCAGGCAU CP023834.1 50S ribosomal protein L2 Escherichia coli K-12 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK P60422 50S ribosomal protein L3 Escherichia coli K-12 0.022277534999999998 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKK MAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA P60438 50S ribosomal protein L4 Escherichia coli K-12 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA P60723 50S ribosomal protein L6 Escherichia coli K-12 0.018932791 1 LEVO MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVT EGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK GVRYADEVVRTKEAKKK P0AG55 50S ribosomal protein L13 Escherichia coli K-12 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI P0AA10 50S ribosomal protein L14 Escherichia coli K-12 0.013565066999999998 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL P0ADY3 50S ribosomal protein L15 Escherichia coli K-12 0.014879357 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIE P02413 50S ribosomal protein L16 Escherichia coli K-12 0.015312269 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV RMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM P0ADY7 50S ribosomal protein L17 Escherichia coli K-12 0.014393656999999999 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE P0AG44 50S ribosomal protein L18 Escherichia coli K-12 0.012794667999999999 1 LEVO MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF P0C018 50S ribosomal protein L19 Escherichia coli K-12 0.013159278 1 LEVO MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPV VDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN P0A7K6 50S ribosomal protein L20 Escherichia coli K-12 0.013528024 1 LEVO MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFI NGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA P0A7L3 50S ribosomal protein L21 Escherichia coli K-12 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA P0AG48 50S ribosomal protein L22 Escherichia coli K-12 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR P61175 50S ribosomal protein L23 Escherichia coli K-12 0.01122216 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNLDFVGGAE P0ADZ0 50S ribosomal protein L24 Escherichia coli K-12 0.011339249999999999 1 LEVO MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA DRVGFRFEDGKKVRFFKSNSETIK P60624 50S ribosomal protein L25 Escherichia coli K-12 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA P68919 50S ribosomal protein L27 Escherichia coli K-12 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE P0A7L8 50S ribosomal protein L28 Escherichia coli K-12 0.009027550999999998 1 LEVO MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY P0A7M2 50S ribosomal protein L29 Escherichia coli K-12 0.0072864639999999994 1 LEVO MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA P0A7M6 50S ribosomal protein L30 Escherichia coli K-12 0.006554819999999999 1 LEVO MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE P0AG51 50S ribosomal protein L32 Escherichia coli K-12 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK P0A7N4 50S ribosomal protein L33 Escherichia coli K-12 0.006388631 1 LEVO MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK P0A7N9 50S ribosomal protein L34 Escherichia coli K-12 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK P0A7P5 50S ribosomal protein L35 Escherichia coli K-12 0.007313032 1 LEVO MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA P0A7Q1 50S ribosomal protein L36 Escherichia coli K-12 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG P0A7Q6 Myxovalargin A Myxococcus fulvus 0.001678092 1 LEVO (IVA)(RXL)A(MAA)(DVA)(DVA)(IB9)(DVA)(RXL)(DAR)V(DVA)(RX9)(DAL)(DHV)(AG2) MAGNESIUM ION 2.4305e-05 145 MG ZINC ION 6.5409e-05 1 ZN water 1.8015e-05 28 HOH singleParticle particle 7.5 0.05 C8H18N2O4S Hepes 0.1 CH3CO2K Potassium acetate 0.08 NH4Cl Ammonium chloride 0.025 C4H6MgO4 Magnesium acetate 0.002 C4H10O2S2 Dithiothreitol 0.01 C24H46O11 DDM

Solutions were made fresh, pH was adjusted with potassium hydroxide at 4 degrees celcius and sterile filtered.

Quantifoil R3/3 COPPER 300 CARBON HOLEY 300.0 ETHANE-PROPANE 100 277 FEI VITROBOT MARK IV

2 seconds blotting before plunging..

7 OD(A260/mL) were applied to the grid.

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.0 3.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GATAN K2 SUMMIT (4k x 4k) COUNTING 44.0 1 680054 4YBB

High-resolution structure of the Escherichia coli ribosome

3 C1 FOURIER SPACE 2.1 FSC 0.143 CUT-OFF RELION 3.1 580425 ANGULAR RECONSTITUTION RELION 3.1 ANGULAR RECONSTITUTION RELION 3.1 6 RELION 3.1 4YBB PDB experimental model RIGID BODY FIT Correlation coefficient emd_14121_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 298.08002 298.08002 298.08002 90.0 90.0 90.0 X Y Z -0.023934202 0.10761386 0.0006184802 0.004725839 0.82800007 0.82800007 0.82800007 AUTHOR ::::EMDATABANK.org::::EMD-14121:::: 3D refined map emd_14121_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 298.08002 298.08002 298.08002 90.0 90.0 90.0 X Y Z -0.1630209 0.37974817 0.00061849563 0.020345245 0.82800007 0.82800007 0.82800007 AUTHOR ::::EMDATABANK.org::::EMD-14121:::: post processed map emd_14121_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 298.08002 298.08002 298.08002 90.0 90.0 90.0 X Y Z -0.04020801 0.14146574 0.000618475 0.0069265445 0.82800007 0.82800007 0.82800007 AUTHOR ::::EMDATABANK.org::::EMD-14121:::: Half map 1 emd_14121_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 298.08002 298.08002 298.08002 90.0 90.0 90.0 X Y Z -0.04356209 0.13384698 0.0006185162 0.0069389 0.82800007 0.82800007 0.82800007 AUTHOR ::::EMDATABANK.org::::EMD-14121:::: Half map 2