Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit

2025-03-12 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REFINEMENT_DESCRIPTION chem_comp_atom chem_comp_bond citation refine _citation.journal_volume _citation.page_first _citation.page_last _refine.ls_d_res_high _refine.ls_d_res_low STRUCTURE_SUMMARY em_admin pdbx_entry_details pdbx_modification_feature _em_admin.last_update _pdbx_entry_details.has_protein_modification 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 PDBe PDBe 2022-08-05 2023-03-08 2023-03-08 2025-03-12 Other government DLR01Kl1820 Germany Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit Koller TO Morici M Wilson DN E.coli, Drosocin, Dro1, antimicrobial peptide, proline-rich, PrAMP, 50S, RIBOSOME Koller TO Morici M Berger M Safdari HA Lele DS Beckert B Kaur KJ Wilson DN Structural basis for translation inhibition by the glycosylated drosocin peptide. Nat.Chem.Biol. US 19 1072 1081 2023 36997646 doi:10.1038/s41589-023-01293-7 1552-4469 EMD-15488 other EM volume

Drosocin bound to the terminating ribosome

EMD-15523 other EM volume

Drosocin bound to the elongating ribosome

8ana FULLOVERLAP Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit Cryo-EM structure of the proline-rich antimicrobial peptide drosocin bound to the 50S ribosomal subunit 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 Escherichia coli K-12 1.5 50S ribosomal protein L33 Escherichia coli BW25113 0.006388631 1 LEVO MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK A0A3S5YPG8 50S ribosomal protein L34 Escherichia coli BW25113 0.005397463 1 LEVO MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK A0A8X6EVB8 50S ribosomal protein L35 Escherichia coli BW25113 0.007313032 1 LEVO MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA A0A8S0FT45 50S ribosomal protein L36 Escherichia coli BW25113 0.00437739 1 LEVO MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG A0A2X1PTA3 50S ribosomal protein L31 Escherichia coli BW25113 0.007887116999999999 1 LEVO MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK C3SIV2 Drosocin1 Drosophila melanogaster 0.002204579 1 LEVO GKPRPYSPRPTSHPRPIRV B4MNS1 23S ribosomal RNA Escherichia coli BW25113 0.941463375 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 CGCGGCAAGACGGAAAGACCCCGU(G7M)AACCUUUACUAUAGCUUGACACUGAACAUUGGACCUUGAUGUGUAGGAUAG GUGGGAGGCUUUGAAGUGUGGACGCCAGUCUGCAUGGAGCCGACCUUGAAAUACCACCCUUUAAUGUUUGAUGUUCUAAC GUUGACCCCUAAUCGGGGUUGCGGACAGUGUCUGGUGGGUAGUUUGACUG(OMG)GGCGGUCUCCUCCUAAAGAGUAACG GAGGAGCACGAAGGUUGGCUAAUCCUGGUCGGACAUCAGGAGGUUAGUGCAAUGGCAUAAGCCAGCUUGACUGCGAGCGU GACGGCGCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAG GUACUCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCA(OMC)CU CG(2MA)(PSU)GUCGGCUCAUCACAUCCUGGGGCUGAAGUAGGUCCCAAGGGUAUGGC(OMU)GUUCGCCAUUUAAAGU GGUACGCGAGC(PSU)GGGUUUAGAACGUCGUGAGACAG(PSU)(PSU)CGGUCCCUAUCUGCCGUGGGCGCUGGAGAAC UGAGGGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGCAUCACUGGUGUUCGGGUUGUCAUGCCAAUGGCACUGCC CGGUAGCUAAAUGCGGAAGAGAUAAGUGCUGAAAGCAUCUAAGCACGAAACUUGCCCCGAGAUGAGUUCUCCCUGACCCU UUAAGGGUCCUGAAGGAACGUUGAAGACGACGACGUUGAUAGGCCGGGUGUGUAAGCGCAGCGAUGCGUUGAGCUAACCG GUACUAAUGAACCGUGAGGCUUAACCU 5S ribosomal RNA Escherichia coli BW25113 0.03879008999999999 1 UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGU GUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU 50S ribosomal protein L2 Escherichia coli BW25113 0.029923619 1 LEVO MAVVKCKPTSPGRRHVVKVVNPELHKGKPFAPLLEKNSKSGGRNNNGRITTRHIGGGHKQAYRIVDFKRNKDGIPAVVER LEYDPNRSANIALVLYKDGERRYILAPKGLKAGDQIQSGVDAAIKPGNTLPMRNIPVGSTVHNVEMKPGKGGQLARSAGT YVQIVARDGAYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVDHPHGGGEGRNF GKHPVTPWGVQTKGKKTRSNKRTDKFIVRRRSK A0A7L6YWH1 50S ribosomal protein L3 Escherichia coli BW25113 0.022291562 1 LEVO MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLW EFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQN(MEQ)TPGKVF KGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA C3SQU2 50S ribosomal protein L4 Escherichia coli BW25113 0.022121566 1 LEVO MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRS GGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLA ARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA D8A1N0 50S ribosomal protein L5 Escherichia coli BW25113 0.020333611 1 LEVO MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIR QGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTA KSDEEGRALLAAFDFPFRK D6IEK6 50S ribosomal protein L6 Escherichia coli BW25113 0.018932791 1 LEVO MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVT EGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGK GVRYADEVVRTKEAKKK C3SR17 50S ribosomal protein L9 Escherichia coli BW25113 0.01578902 1 LEVO MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTI ASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE C3SFP2 50S ribosomal protein L13 Escherichia coli BW25113 0.016050606 1 LEVO MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGH IGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI A0A656YGQ7 50S ribosomal protein L14 Escherichia coli BW25113 0.013565066999999998 1 LEVO MIQEQTMLNVADNSGARRVMCIKVLGGSHRRYAGVGDIIKITIKEAIPRGKVKKGDVLKAVVVRTKKGVRRPDGSVIRFD GNACVLLNNNSEQPIGTRIFGPVTRELRSEKFMKIISLAPEVL C3SQZ2 50S ribosomal protein L15 Escherichia coli BW25113 0.015008470999999999 1 LEVO MRLNTLSPAEGSKKAGKRLGRGIGSGLGKTGGRGHKGQKSRSGGGVRRGFEGGQMPLYRRLPKFGFTSRKAAITAEIRLS DLAKVEGGVVDLNTLKAANIIGIQIEFAKVILAGEVTTPVTVRGLRVTKGARAAIEAAGGKIEE P02413 50S ribosomal protein L16 Escherichia coli BW25113 0.015312269 1 LEVO MLQPKRTKFRKMHKGRNRGLAQGTDVSFGSFGLKAVGRGRLTARQIEAARRAMTRAVKRQGKIWIRVFPDKPITEKPLAV RMGKGKGNVEYWVALIQPGKVLYEMDGVPEELAREAFKLAAAKLPIKTTFVTKTVM A0A0H3EMH6 50S ribosomal protein L17 Escherichia coli BW25113 0.014393656999999999 1 LEVO MRHRKSGRQLNRNSSHRQAMFRNMAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLF NELGPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDRSEKAEAAAE A0A1X3JBW6 50S ribosomal protein L18 Escherichia coli BW25113 0.012794667999999999 1 LEVO MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAEQLKYTGNKDAAAAVGKAVAE RALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF A0A514EKV0 50S ribosomal protein L19 Escherichia coli BW25113 0.013159278 1 LEVO MSNIIKQLEQEQMKQDVPSFRPGDTVEVKVWVVEGSKKRLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERVFQTHSPV VDSISVKRRGAVRKAKLYYLRERTGKAARIKERLN A0A370V6W8 50S ribosomal protein L20 Escherichia coli BW25113 0.013528024 1 LEVO MARVKRGVIARARHKKILKQAKGYYGARSRVYRVAFQAVIKAGQYAYRDRRQRKRQFRQLWIARINAAARQNGISYSKFI NGLKKASVEIDRKILADIAVFDKVAFTALVEKAKAALA A0A378BCJ4 50S ribosomal protein L21 Escherichia coli BW25113 0.011586374 1 LEVO MYAVFQSGGKQHRVSEGQTVRLEKLDIATGETVEFAEVLMIANGEEVKIGVPFVDGGVIKAEVVAHGRGEKVKIVKFRRR KHYRKQQGHRQWFTDVKITGISA A0A0E2L2H1 50S ribosomal protein L22 Escherichia coli BW25113 0.012253359 1 LEVO METIAKHRHARSSAQKVRLVADLIRGKKVSQALDILTYTNKKAAVLVKKVLESAIANAEHNDGADIDDLKVTKIFVDEGP SMKRIMPRAKGRADRILKRTSHITVVVSDR A0A0F6B7N1 50S ribosomal protein L23 Escherichia coli BW25113 0.01122216 1 LEVO MIREERLLKVLRAPHVSEKASTAMEKSNTIVLKVAKDATKAEIKAAVQKLFEVEVEVVNTLVVKGKVKRHGQRIGRRSDW KKAYVTLKEGQNLDFVGGAE D7Y3D8 50S ribosomal protein L24 Escherichia coli BW25113 0.011339249999999999 1 LEVO MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKA DRVGFRFEDGKKVRFFKSNSETIK S1E9P3 50S ribosomal protein L25 Escherichia coli BW25113 0.010713465 1 LEVO MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRH PYKPKLQHIDFVRA P68919 50S ribosomal protein L27 Escherichia coli BW25113 0.00914654 1 LEVO MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFI SIEAE C3SSG7 50S ribosomal protein L28 Escherichia coli BW25113 0.009027550999999998 1 LEVO MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY C3SME2 50S ribosomal protein L29 Escherichia coli BW25113 0.0072864639999999994 1 LEVO MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA P0A7M6 50S ribosomal protein L30 Escherichia coli BW25113 0.006554819999999999 1 LEVO MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE C3SR32 50S ribosomal protein L32 Escherichia coli BW25113 0.006463444999999999 1 LEVO MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK A0A657HW13 ZINC ION 6.5409e-05 2 ZN 2-acetamido-2-deoxy-alpha-D-galactopyranose 0.000221208 1 A2G MAGNESIUM ION 2.4305e-05 216 MG SPERMINE 0.00020234 1 SPM water 1.8015e-05 42 HOH singleParticle particle 7.4 50.0 C8H18N2O4S HEPES 100.0 C2H3KO2 Potassiumacetate 25.0 C4H6MgO4 Magnesiumacetate Quantifoil R3/3 COPPER CARBON HOLEY 3.0 ETHANE-PROPANE 100 278 FEI VITROBOT MARK IV

8 OD260/mL

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.4 0.9 FEI FALCON IV (4k x 4k) 40.0 1 EMD-12573 2.1 FSC 0.143 CUT-OFF 159749 ANGULAR RECONSTITUTION RELION 4.0 Beta ANGULAR RECONSTITUTION RELION 4.0 beta 6 100000.0 RELION 4.0 beta emd_15533.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 480.0 480.0 480.0 90.0 90.0 90.0 X Y Z -0.034172185 0.11462202 0.00009906522 0.0017050977 0.8 0.8 0.8 0.012 AUTHOR ::::EMDATABANK.org::::EMD-15533:::: post masked emd_15533_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 480.0 480.0 480.0 90.0 90.0 90.0 X Y Z -0.029322376 0.08138945 -0.00005529084 0.0036879552 0.8 0.8 0.8 AUTHOR ::::EMDATABANK.org::::EMD-15533:::: half 1 emd_15533_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 600 600 600 0 0 0 600 600 600 480.0 480.0 480.0 90.0 90.0 90.0 X Y Z -0.02732311 0.083624534 -0.000055338358 0.0036753213 0.8 0.8 0.8 AUTHOR ::::EMDATABANK.org::::EMD-15533:::: half 2