2025-05-21 REL PDBe INITIAL_RELEASE REPOSITORY PDBe PDBe 2024-10-29 2025-05-21 2025-05-21 2025-05-21 Other government DLR01Kl1820 German Research Foundation (DFG) SPP1879 (DFG WI3285/5-2) Germany Cryo-EM structure of the Vibrio natrigens 50S ribosomal subunit in complex with the proline-rich antimicrobial peptide Bac5(1-17). Raulf KF Koller TO Beckert B Morici M Lepak A Bange G Wilson DN Vibrio natriegens, Ribosome, Bac5, Bactenecin 5, 50S, V. natriegens Raulf K Koller TO Beckert B Lepak A Morici M Mardirossian M Scocchi M Bange G Wilson DN The structure of the Vibrio natriegens 70S ribosome in complex with the proline-rich antimicrobial peptide Bac5(1-17). Nucleic Acids Res. UK 53 2025 40331629 doi:10.1093/nar/gkaf324 1362-4962 0389 NARHAD 9h91 FULLOVERLAP Structure of the Proline-rich Antimicrobial Peptide Bac5(1-17) in Complex with the Vibrio natriegens 50S ribosomal subunit Structure of the Proline-rich Antimicrobial Peptide Bac5(1-17) in Complex with the Vibrio natriegens 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 Vibrio natriegens 50S ribosomal protein L32 Vibrio natriegens 0.0063142319999999995 1 LEVO MAVQKNRKTRSKRGMRRSHDALTTAALSVDATSGETHLRHNVTAEGYYRGKKVINK A0AAN0Y2T2 50S ribosomal protein L33 Vibrio natriegens 0.0065407899999999995 1 LEVO MAKKGVREKIRLVSSAGTGHFYTTDKNKRNMPGKFEIKKFDPVVRQHVMYKEAKIK A0AAN0XZW0 50S ribosomal protein L34 Vibrio natriegens 0.005198317 1 LEVO MKRTFQPTVLKRKRTHGFRARMATKNGRKVINARRAKGRARLSK A0AAN0Y4Q5 50S ribosomal protein L35 Vibrio natriegens 0.007324994 1 LEVO MPKMKTNKGAAKRFKKTAGGIKYKHATKRHILTKRTTKNKRQLRPNAILPKCEVAAVIRMLPYA A0AAN0Y2A7 50S ribosomal protein L36 Vibrio natriegens 0.0042913 1 LEVO MKVRASVKKICRNCKVIKRNGVVRVICSEPKHKQRQG A0AAN0Y149 Cathelicidin-2 Bos taurus 0.002167625
Bactenecin-5 (1-17)
1 LEVO RFRPPIRRPPIRPPFYP P19660 5S ribosomal RNA Vibrio natriegens 0.03899016 1 UGCUUGGCGACCAUAGCGUUUUGGACCCACCUGACUUCCAUUCCGAACUCAGAAGUGAAACGAAAUAGCGCCGAUGGUAG UGUGGGGUUUCCCCAUGUGAGAGUAGGACAUCGCCAGGCAA 50S ribosomal protein L2 Vibrio natriegens 0.030059688999999997 1 LEVO MAIVKCKPTSPGRRHVVKVVNADLHKGKPYAPLLEKNSKNGGRNNNGRITVRHIGGGHKHHYRVIDFKRTKDGIPATVER LEYDPNRSANIALVLYKDGERRYILAPKGVVAGDVVQSGVDAPIKAGNTLPMRNIPVGSTVHNVELKPGKGGQLARSAGA YAQIVARDGTYVTIRLRSGEMRKVLSEGRATIGEVGNSEHMLRELGKAGATRWRGVRPTVRGVVMNPVDHPHGGGEGRTS GGRHPVSPWGMPTKGYKTRKNKRTDKYIVRRRNK A0AAN1CUJ7 50S ribosomal protein L3 Vibrio natriegens 0.022393613 1 LEVO MIGLIGRKVGMTRVFTEDGVSIPVTVVEVEANRVSQVKTLETDGYAAIQVTAGAKKANRVNKAEAGHFAKAGVEAGRGLW EFRLENGEEFEVGSELTVELFNETKKVDVTGTSKGKGFQGAVKRWNFRTQDMTHGNSLSHRAPGSIGQCQTPGRVFKGKK MAGHMGAERVTTQNLEIVRVDAERNLLLIKGAVPGATGGNVIVKPAVKA A0AAN1CUL8 50S ribosomal protein L4 Vibrio natriegens 0.021906223000000002 1 LEVO MELMVKGADALTVSETTFGREFNEALVHQVVVAYAAGARQGTRAQKTRSEVSGGGAKPWRQKGTGRARAGTIRSPIWRSG GVTFAAKPQDHSQKVNKKMYRGAMKSILSELVRQERLIVVDNFSVEAPKTKELVAKLKELELTDALIVTSEVDENLFLAA RNLYKVDARDVAGIDPVSLIAFDKVVMTAEAVKQVEEMLA A0AAN1CVG6 50S ribosomal protein L6 Vibrio natriegens 0.018801609 1 LEVO MSRVAKAPVAIPAGVEVKLNGQEITVKGAKGELTRVLNDAVVIAQEENNLTFGPKEGVVNAWAQAGTARALVNNMVVGVT EGFTKKLTLKGVGYRAAIKGNAVGLTLGFSHPVEHELPAGIKAECPSQTEIVITGADKQLVGQVAADIRSYRQPEPYKGK GVRYADENVRTKEAKKK A0AAN1CUM2 Large ribosomal subunit protein bL9 Vibrio natriegens 0.015769948 1 LEVO MQVILLDKIGNLGGLGDTVNVKSGYARNFLIPQGKAVMATKGNVEMFEARRAELEAKVAEQLTAAEARAEKVNALEAVVI ASKAGDEGKLFGSIGTRDIADAITAAGVEVAKSEVRLPEGALRTTGEFEISVQLHSEVFATVNLQVVAAE A0AAN0Y4G6 50S ribosomal protein L13 Vibrio natriegens 0.015990626 1 LEVO MKTFVAKPETVKRDWYVVDAEGKTLGRLASEIASRLRGKHKAEYTPHVDAGDYIIVINAEKVAVTGNKAKDKVYYRHSEF PGGLKSITFEKLIDRKPEMVLELAVKGMLPRGPLGRAMYRKLKVYAGAEHNHVAQQPQVLDI A0AAN0Y0U3 50S ribosomal protein L14 Vibrio natriegens 0.013594068999999999 1 LEVO MIQMQSMLDAADNSGARSVMCIKVLGGSHRRYAHIGDVIKVTVKEAIPRGKVKKGDVLKAVVVRTRKGVRRPDGSVIRFD RNACVLLNDNTEQPIGTRIFGPVTRELRGDKFMKIVSLAPEVL A0AAN0Y0F6 50S ribosomal protein L15 Vibrio natriegens 0.014878357 1 LEVO MRLNTLAPAAGAKTSAKRVGRGIGSGLGKTGGRGHKGQKSRSGGSVRPGFEGGQMPLKQRLPKFGFTSRKSLVSAEVRLA ELAKVSGDVVDLNSLKAANIITKNIEFVKVVLSGEINKAVTVKGLRVTKGAKAAIEAAGGKIEE A0AAN1CUX1 50S ribosomal protein L16 Vibrio natriegens 0.015557379999999999 1 LEVO MLQPKRTKFRKVQTGRNRGLAKGTDVSFGEFGLKAVGRGRLTARQIEAARRAMTRHVKRQGKIWIRVFPDKPITEKPLEV RQGKGKGNVEYWVAQIQPGKVMYEMGGVPEELAREAFRLAARKLPFKTTFVTKQVM A0AAN0Y0C5 50S ribosomal protein L17 Vibrio natriegens 0.014231482 1 LEVO MRHRKSGRQLNRNSSHRKAMFSNMASSLVRHEVIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEVVAKLF NELGPRFAARQGGYTRILKAGFRAGDKAPMAYIELVDRPAAEEAAE A0AAN0Y071 50S ribosomal protein L18 Vibrio natriegens 0.012641557 1 LEVO MDKKASRIRRATRARRKIAELGATRLVVHRTPRHVYAQVIAANGSEVIAAASTVEKAIREQVKYTGNVDAAKAVGKAVAE RALEKGVTAVAFDRSGFQYHGRVAALAESAREAGLKF A0AAN1CVH0 50S ribosomal protein L19 Vibrio natriegens 0.013305461 1 LEVO MSNIIKALEEEQMKSDLPKFAPGDTVVVQVKVKEGDRERLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERTFQTHSPI VDSIEVKRRGAVRRAKLYYLRERSGKSARIKEKLAKK A0AAN1CWW0 50S ribosomal protein L20 Vibrio natriegens 0.013414822 1 LEVO MPRVKRGVQARARHKKVLKQAKGYYGARSRVYRVAFQAVTKAGQYAYRDRRAKKRQFRQLWIARINAASRQNGLSYSRFI NGLKKASIEIDRKILADIAVFDKAAFAVLVEKAKAAL A0AAN1CVB0 50S ribosomal protein L21 Vibrio natriegens 0.011544295999999999 1 LEVO MYAVFQSGGKQHRVSEGQTLRLEKLDVETGATVEFDKVLLVANGEDIKVGAPLVEGGKIVAEVVQHGRGDKVKIVKFRRR KHSRKQQGHRQWFTEVKITGINA A0AAN1CVI2 50S ribosomal protein L22 Vibrio natriegens 0.012181115999999999 1 LEVO MEAIAKHNFARISPQKARLVADQIRGKSVDQALEILTFSNKKAAELVKKVLESAIANAEHNEGADIDDLNVAKIFVDEGP TMKRIMPRAKGRADRILKRSSHITVVVADR A0AAN0Y0L0 50S ribosomal protein L23 Vibrio natriegens 0.011151074 1 LEVO MITEERILKVLRAPHISEKATMAAEKANTIVFKVAKDATKKEIKAAVEKLFEVEVKSVNTLITKGKTKRQGLRQGRRSDV KKAYVTLKEGQDLDFVGGAE A0AAN1CUR9 50S ribosomal protein L24 Vibrio natriegens 0.011239045 1 LEVO MAAKIRRNDEVIVLAGKDKGKKGKVTKVLATGKVIVEGINLVKKHQKPVPALGQQGGIVEQEAAIDASNVAIFNAATGKA DRIGFRFEDGKKVRFFKSNGETVSN A0AAN0Y061 50S ribosomal protein L25 Vibrio natriegens 0.010391019 1 LEVO MKFEAVVRTELGKGASRRLRHAGKFPAVVYGGEEAAVAIVLNHDDIVNQMDKPEFYEGIVLVIDGKEVSVKPQDVQRHAF KPKVEHMDFIRI A0AAN0Y4S6 50S ribosomal protein L27 Vibrio natriegens 0.009228595999999999 1 LEVO MAHKKAGGSTRNGRDSESKRLGVKRFGGESVLAGNIIVRQRGTKFHAGNNVGIGKDHTLFALTEGKVKFEVKGPKNRKFV SIEAE A0AAN1CUT7 50S ribosomal protein L28 Vibrio natriegens 0.009056614999999999 1 LEVO MSRVCQVTGKRPVTGNNRSHARNATKRRFLPNLQTHRFWVESEKRFVKLRLSAKGMRIIDKKGIDTVLADMRARGENV A0AAN0Y076 50S ribosomal protein L29 Vibrio natriegens 0.007205346999999999 1 LEVO MKAQDLREKSVEELNAELMNLLREQFNLRMQAATGQLQQTHTLKAVRRDIARVKTVLTEKAGA A0AAN0XZZ8 50S ribosomal protein L30 Vibrio natriegens 0.006596873 1 LEVO MATIKVTQTKSSIGRLPKHKATLRGLGLRKINHTVELEDTPCVRGMINKVYYMVKVEE A0AAN1CUK2 23S ribosomal RNA Vibrio natriegens 0.881521312 1 GGUUAAGUGACUAAGCGUACACGGUGGAUGCCUUGGCAGUCAGAGGCGAUGAAGGACGUAUUAACUUGCGAUAAGCCCAG AUUAGGCAGUAAAAGCCACUUGAGUCUGGGAUUUCCGAAUGGGGAAACCCACUUACAUAAGUAAGUAUCCUGUUGUGAAU ACAUAGCAACAGGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCGAAAG UAGCGGCGAGCGAAAUUGGACUAGCCCUUAAGCUUUACACACGUUAGACGAACGGUCUGGAAAGGCCGACGAUACAGGGU GAUAGUCCCGUAGUUGACGAUGUGUGUUCAGUGAAAUCGAGUAGGGCGGGACACGUGAUAUCCUGUCUGAAUAUGGGGGG ACCAUCCUCCAAGGCUAAAUACUACUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCUGUG AGGGGAGUGAAAUAGAACCUGAAACCGUGUACGUACAAGCAGUAGGAGCAGGCUUGUCCUGUGACUGCGUACCUUUUGUA UAAUGGGUCAGCGACUUAUAUUCAGUGGCAAGGUUAACCAUCUAGGGGAGCCGUAGGGAAACCGAGUCUUAACUGGGCGU UCAGUCUCUGGAUAUAGACCCGAAACCAGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGAGUAACAUCAACUGGAGGACC GAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUAGGGGUGAAAGGCCAAUCAAACCUGGAGAUAGCUGGUUC UCCCCGAAAGCUAUUUAGGUAGCGCCUCGGACGAAUACUACUGGGGGUAGAGCACUGUUAAGGCUAGGCAACCCUUUGCA AACUCCGAAUACCAGUAAGUACUAUCCGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGGAGAGGGAAACAACCCAGA CCGCCAGCUAAGGUCCCAAAUUACUACUAAGUGGGAAACGAUGUGGGAAGGCUCAGACAGAGUCGGCCUGCGCGGAAGAU GUAACGGGGCUAAGUAGUAAACCGAAGCUGCGGCAAUACUAGUAUUGGGUAGGGGAGCGUUCUGUAAGCGGUUGAAGGUG UGUGGUAACGCAUGCUGGACGUAUCAGAAGUGCGAAUGCUGACAUGAGUAACGAUAAAGGGGGUGAAAAACCUCCUCGCC GGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUAAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGA UGGGAAACGGGUUAAUAUUCCCGUACUUCUUACAAUUGCGAUGGGGGGACGGAGAAGGCUAGGUGGGCCUGGCGACGGUU GUCCAGGUUCAAGUGCGUAGGCUUGAGAGUUAGGUAAAUCCGGCUCUCUCUAAGGCUGAGACACGACGUCGAGCACCUAC GGGUGUGAAGUCAUUGAUGCCAUGCUUCCAGGAAAAGCCUCUAAGCUUCAGAUUGUAAGGAAUCGUACCCCAAACCGACA CAGGUGGUCGGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUACCGUAACUUCGG GAGAAGGUACGCUCUCGACGGUGAAGUCCCUCGCGGAUGGAGCUAUUGAGAGUCGCAGAUACCAGGUGGCUGCAACUGUU UAUUAAAAACACAGCACUGUGCAAAAUCGUAAGAUGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGA UGGGGUUAGACUUCGGUCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGA AAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCACGCUGUCUCCACCCGAGACUCAGUGAAAU UGAAAUCGCUGUGAAGAUGCAGUGUACCCGCGGCUAGACGGAAAGACCCCGUGAACCUUUACUACAGCUUGGCACUGAAC AUUGACCCUGUGUUGAUGUUCUAACGUUGACCCCUUAUCGGGGUUGCGGACAGUGCCUGGUGGGUAGUUUGACUGGGGCG GUCUCCUCCCAAAGCGUAACGGAGGAGCACGAAGGUGGGCUAAUCACGGUUCGUGAGGUUAGUGCAAUGGCAUAAGCCCG CUUGACUGCGAGAAUGACAAUUCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCG CUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUC GAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUCGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUG GGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGUUGGAGAAUUGAAAGGGGCUGCUCCUAGUACGAG AGGACCGGAGUGGACGAACCUCUGGUGUUCGGGUUGUGUCGCCAGACGCAUUGCCCGGUAGCUAAGUUCGGGAUCGAUAA CCGCUGAAAGCAUCUAAGCGGGAAGCGAGCCUUGAGAUGAGUUCUCCCUGAUACUUUAAGUAUCCUAAAGGGUUGUCGUA GACUACGACGUUGAUAGGCAGGGUGUGUAAGCGUUGUGAGGCGUUGAGCUAACCUGUACUAAUUGCCCGUGAGGCUUAAC C ZINC ION 6.5409e-05 1 ZN water 1.8015e-05 18 HOH singleParticle particle 7.5 20.0 HEPES 9.0 Magnesium acetate 5.0 Potassium phosphate 95.0 Potassium glutamate 5.0 Ammonium chloride 0.5 Calcium chloride 1.0 Spermidine 8.0 Putrescine 1.0 Dithiothreitol ETHANE-PROPANE 100 277
8 OD/ml ribosome concentration
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.7000000000000001 1.2 FEI FALCON II (4k x 4k) COUNTING 1.0 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 7K00 2.7 FSC 0.143 CUT-OFF 294068 ANGULAR RECONSTITUTION ANGULAR RECONSTITUTION emd_51947.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 441.376 441.376 441.376 90.0 90.0 90.0 X Y Z -0.30411914 0.60020256 0.00022640752 0.013089249 1.061 1.061 1.061 0.055 AUTHOR post processed masked map RIGID BODY FIT emd_51947_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 441.376 441.376 441.376 90.0 90.0 90.0 X Y Z -0.30411914 0.60020256 0.0000868396 0.0194938 1.061 1.061 1.061 AUTHOR post processed map emd_51947_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 441.376 441.376 441.376 90.0 90.0 90.0 X Y Z -0.020910345 0.069653966 0.00008775638 0.0030311719 1.061 1.061 1.061 AUTHOR 3D refined map emd_51947_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 441.376 441.376 441.376 90.0 90.0 90.0 X Y Z -0.022538554 0.07326812 0.00009139524 0.0033423207 1.061 1.061 1.061 AUTHOR Half map 2 emd_51947_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 416 416 416 0 0 0 416 416 416 441.376 441.376 441.376 90.0 90.0 90.0 X Y Z -0.022228008 0.07350996 0.00008228396 0.0033401821 1.061 1.061 1.061 AUTHOR Half map 1