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9H91

Cryo-em structure of the vibrio natrigens 50s ribosomal subunit in complex with the proline-rich antimicrobial peptide bac5(1-17).

PDB DOI: 10.2210/pdb9h91/pdb

Classification: RIBOSOME
Organism(s): Vibrio Natriegens , Synthetic Construct

Deposited: 2024-10-29
Deposition Author(s): Bange, G. , Beckert, B. , Koller, T.O. , Lepak, A. , Morici, M. , Raulf, K.F. , Wilson, D.N.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.7 Å

9h91
Literature

Cryo-em structure of the vibrio natrigens 50s ribosomal subunit in complex with the proline-rich antimicrobial peptide bac5(1-17).

Bange, G. , Beckert, B. , Koller, T.O. , Lepak, A. , Morici, M. , Raulf, K.F. , Wilson, D.N.

Primary Citation of Related Structures: 9H91


Proteins
Molecule Chains Sequence Length Organism Sequence
50S ribosomal protein L32 0 56 Vibrio Natriegens , Synthetic Construct MAVQKNRKTRSKRGMRRSHDALTTAALSVDATSGETHLRHNVTAEGYYRGKKVINK
50S ribosomal protein L4 E 200 Vibrio Natriegens , Synthetic Construct MELMVKGADALTVSETTFGREFNEALVHQVVVAYAAGARQGTRAQKTRSEVSGGGAKPWRQKGTGRARAGTIRSPIWRSGGVTFAAKPQDHSQKVNKKMYRGAMKSILSELVRQERLIVVDNFSVEAPKTKELVAKLKELELTDALIVTSEVDENLFLAARNLYKVDARDVAGIDPVSLIAFDKVVMTAEAVKQVEEMLA
50S ribosomal protein L6 G 177 Vibrio Natriegens , Synthetic Construct MSRVAKAPVAIPAGVEVKLNGQEITVKGAKGELTRVLNDAVVIAQEENNLTFGPKEGVVNAWAQAGTARALVNNMVVGVTEGFTKKLTLKGVGYRAAIKGNAVGLTLGFSHPVEHELPAGIKAECPSQTEIVITGADKQLVGQVAADIRSYRQPEPYKGKGVRYADENVRTKEAKKK
Large ribosomal subunit protein bL9 H 150 Vibrio Natriegens , Synthetic Construct MQVILLDKIGNLGGLGDTVNVKSGYARNFLIPQGKAVMATKGNVEMFEARRAELEAKVAEQLTAAEARAEKVNALEAVVIASKAGDEGKLFGSIGTRDIADAITAAGVEVAKSEVRLPEGALRTTGEFEISVQLHSEVFATVNLQVVAAE
50S ribosomal protein L13 J 142 Vibrio Natriegens , Synthetic Construct MKTFVAKPETVKRDWYVVDAEGKTLGRLASEIASRLRGKHKAEYTPHVDAGDYIIVINAEKVAVTGNKAKDKVYYRHSEFPGGLKSITFEKLIDRKPEMVLELAVKGMLPRGPLGRAMYRKLKVYAGAEHNHVAQQPQVLDI
50S ribosomal protein L14 K 123 Vibrio Natriegens , Synthetic Construct MIQMQSMLDAADNSGARSVMCIKVLGGSHRRYAHIGDVIKVTVKEAIPRGKVKKGDVLKAVVVRTRKGVRRPDGSVIRFDRNACVLLNDNTEQPIGTRIFGPVTRELRGDKFMKIVSLAPEVL
50S ribosomal protein L15 L 144 Vibrio Natriegens , Synthetic Construct MRLNTLAPAAGAKTSAKRVGRGIGSGLGKTGGRGHKGQKSRSGGSVRPGFEGGQMPLKQRLPKFGFTSRKSLVSAEVRLAELAKVSGDVVDLNSLKAANIITKNIEFVKVVLSGEINKAVTVKGLRVTKGAKAAIEAAGGKIEE
50S ribosomal protein L16 M 136 Vibrio Natriegens , Synthetic Construct MLQPKRTKFRKVQTGRNRGLAKGTDVSFGEFGLKAVGRGRLTARQIEAARRAMTRHVKRQGKIWIRVFPDKPITEKPLEVRQGKGKGNVEYWVAQIQPGKVMYEMGGVPEELAREAFRLAARKLPFKTTFVTKQVM
50S ribosomal protein L17 N 126 Vibrio Natriegens , Synthetic Construct MRHRKSGRQLNRNSSHRKAMFSNMASSLVRHEVIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEVVAKLFNELGPRFAARQGGYTRILKAGFRAGDKAPMAYIELVDRPAAEEAAE
50S ribosomal protein L18 O 117 Vibrio Natriegens , Synthetic Construct MDKKASRIRRATRARRKIAELGATRLVVHRTPRHVYAQVIAANGSEVIAAASTVEKAIREQVKYTGNVDAAKAVGKAVAERALEKGVTAVAFDRSGFQYHGRVAALAESAREAGLKF
50S ribosomal protein L19 P 117 Vibrio Natriegens , Synthetic Construct MSNIIKALEEEQMKSDLPKFAPGDTVVVQVKVKEGDRERLQAFEGVVIAIRNRGLHSAFTVRKISNGEGVERTFQTHSPIVDSIEVKRRGAVRRAKLYYLRERSGKSARIKEKLAKK
50S ribosomal protein L33 1 56 Vibrio Natriegens , Synthetic Construct MAKKGVREKIRLVSSAGTGHFYTTDKNKRNMPGKFEIKKFDPVVRQHVMYKEAKIK
50S ribosomal protein L20 Q 117 Vibrio Natriegens , Synthetic Construct MPRVKRGVQARARHKKVLKQAKGYYGARSRVYRVAFQAVTKAGQYAYRDRRAKKRQFRQLWIARINAASRQNGLSYSRFINGLKKASIEIDRKILADIAVFDKAAFAVLVEKAKAAL
50S ribosomal protein L21 R 103 Vibrio Natriegens , Synthetic Construct MYAVFQSGGKQHRVSEGQTLRLEKLDVETGATVEFDKVLLVANGEDIKVGAPLVEGGKIVAEVVQHGRGDKVKIVKFRRRKHSRKQQGHRQWFTEVKITGINA
50S ribosomal protein L22 S 110 Vibrio Natriegens , Synthetic Construct MEAIAKHNFARISPQKARLVADQIRGKSVDQALEILTFSNKKAAELVKKVLESAIANAEHNEGADIDDLNVAKIFVDEGPTMKRIMPRAKGRADRILKRSSHITVVVADR
50S ribosomal protein L23 T 100 Vibrio Natriegens , Synthetic Construct MITEERILKVLRAPHISEKATMAAEKANTIVFKVAKDATKKEIKAAVEKLFEVEVKSVNTLITKGKTKRQGLRQGRRSDVKKAYVTLKEGQDLDFVGGAE
50S ribosomal protein L24 U 105 Vibrio Natriegens , Synthetic Construct MAAKIRRNDEVIVLAGKDKGKKGKVTKVLATGKVIVEGINLVKKHQKPVPALGQQGGIVEQEAAIDASNVAIFNAATGKADRIGFRFEDGKKVRFFKSNGETVSN
50S ribosomal protein L25 V 92 Vibrio Natriegens , Synthetic Construct MKFEAVVRTELGKGASRRLRHAGKFPAVVYGGEEAAVAIVLNHDDIVNQMDKPEFYEGIVLVIDGKEVSVKPQDVQRHAFKPKVEHMDFIRI
50S ribosomal protein L27 W 85 Vibrio Natriegens , Synthetic Construct MAHKKAGGSTRNGRDSESKRLGVKRFGGESVLAGNIIVRQRGTKFHAGNNVGIGKDHTLFALTEGKVKFEVKGPKNRKFVSIEAE
50S ribosomal protein L28 X 78 Vibrio Natriegens , Synthetic Construct MSRVCQVTGKRPVTGNNRSHARNATKRRFLPNLQTHRFWVESEKRFVKLRLSAKGMRIIDKKGIDTVLADMRARGENV
50S ribosomal protein L29 Y 63 Vibrio Natriegens , Synthetic Construct MKAQDLREKSVEELNAELMNLLREQFNLRMQAATGQLQQTHTLKAVRRDIARVKTVLTEKAGA
50S ribosomal protein L30 Z 58 Vibrio Natriegens , Synthetic Construct MATIKVTQTKSSIGRLPKHKATLRGLGLRKINHTVELEDTPCVRGMINKVYYMVKVEE
50S ribosomal protein L34 2 44 Vibrio Natriegens , Synthetic Construct MKRTFQPTVLKRKRTHGFRARMATKNGRKVINARRAKGRARLSK
50S ribosomal protein L35 3 64 Vibrio Natriegens , Synthetic Construct MPKMKTNKGAAKRFKKTAGGIKYKHATKRHILTKRTTKNKRQLRPNAILPKCEVAAVIRMLPYA
50S ribosomal protein L36 4 37 Vibrio Natriegens , Synthetic Construct MKVRASVKKICRNCKVIKRNGVVRVICSEPKHKQRQG
Cathelicidin-2 9 17 Vibrio Natriegens , Synthetic Construct RFRPPIRRPPIRPPFYP
50S ribosomal protein L2 C 274 Vibrio Natriegens , Synthetic Construct MAIVKCKPTSPGRRHVVKVVNADLHKGKPYAPLLEKNSKNGGRNNNGRITVRHIGGGHKHHYRVIDFKRTKDGIPATVERLEYDPNRSANIALVLYKDGERRYILAPKGVVAGDVVQSGVDAPIKAGNTLPMRNIPVGSTVHNVELKPGKGGQLARSAGAYAQIVARDGTYVTIRLRSGEMRKVLSEGRATIGEVGNSEHMLRELGKAGATRWRGVRPTVRGVVMNPVDHPHGGGEGRTSGGRHPVSPWGMPTKGYKTRKNKRTDKYIVRRRNK
50S ribosomal protein L3 D 209 Vibrio Natriegens , Synthetic Construct MIGLIGRKVGMTRVFTEDGVSIPVTVVEVEANRVSQVKTLETDGYAAIQVTAGAKKANRVNKAEAGHFAKAGVEAGRGLWEFRLENGEEFEVGSELTVELFNETKKVDVTGTSKGKGFQGAVKRWNFRTQDMTHGNSLSHRAPGSIGQCQTPGRVFKGKKMAGHMGAERVTTQNLEIVRVDAERNLLLIKGAVPGATGGNVIVKPAVKA

Nucleic Acids / Hybrid
Molecule Chains Sequence Length Organism Sequence
23S ribosomal RNA a 2721 NA GGUUAAGUGACUAAGCGUACACGGUGGAUGCCUUGGCAGUCAGAGGCGAUGAAGGACGUAUUAACUUGCGAUAAGCCCAGAUUAGGCAGUAAAAGCCACUUGAGUCUGGGAUUUCCGAAUGGGGAAACCCACUUACAUAAGUAAGUAUCCUGUUGUGAAUACAUAGCAACAGGAGGCGAACCGGGGGAACUGAAACAUCUAAGUACCCCGAGGAAAAGAAAUCAACCGAGAUUCCGAAAGUAGCGGCGAGCGAAAUUGGACUAGCCCUUAAGCUUUACACACGUUAGACGAACGGUCUGGAAAGGCCGACGAUACAGGGUGAUAGUCCCGUAGUUGACGAUGUGUGUUCAGUGAAAUCGAGUAGGGCGGGACACGUGAUAUCCUGUCUGAAUAUGGGGGGACCAUCCUCCAAGGCUAAAUACUACUGACUGACCGAUAGUGAACCAGUACCGUGAGGGAAAGGCGAAAAGAACCCCUGUGAGGGGAGUGAAAUAGAACCUGAAACCGUGUACGUACAAGCAGUAGGAGCAGGCUUGUCCUGUGACUGCGUACCUUUUGUAUAAUGGGUCAGCGACUUAUAUUCAGUGGCAAGGUUAACCAUCUAGGGGAGCCGUAGGGAAACCGAGUCUUAACUGGGCGUUCAGUCUCUGGAUAUAGACCCGAAACCAGGUGAUCUAGCCAUGGGCAGGUUGAAGGUUGAGUAACAUCAACUGGAGGACCGAACCGACUAAUGUUGAAAAAUUAGCGGAUGACUUGUGGCUAGGGGUGAAAGGCCAAUCAAACCUGGAGAUAGCUGGUUCUCCCCGAAAGCUAUUUAGGUAGCGCCUCGGACGAAUACUACUGGGGGUAGAGCACUGUUAAGGCUAGGCAACCCUUUGCAAACUCCGAAUACCAGUAAGUACUAUCCGGGAGACACACGGCGGGUGCUAACGUCCGUCGUGGAGAGGGAAACAACCCAGACCGCCAGCUAAGGUCCCAAAUUACUACUAAGUGGGAAACGAUGUGGGAAGGCUCAGACAGAGUCGGCCUGCGCGGAAGAUGUAACGGGGCUAAGUAGUAAACCGAAGCUGCGGCAAUACUAGUAUUGGGUAGGGGAGCGUUCUGUAAGCGGUUGAAGGUGUGUGGUAACGCAUGCUGGACGUAUCAGAAGUGCGAAUGCUGACAUGAGUAACGAUAAAGGGGGUGAAAAACCUCCUCGCCGGAAGACCAAGGGUUCCUGUCCAACGUUAAUCGGGGCAGGGUAAGUCGACCCCUAAGGCGAGGCCGAAAGGCGUAGUCGAUGGGAAACGGGUUAAUAUUCCCGUACUUCUUACAAUUGCGAUGGGGGGACGGAGAAGGCUAGGUGGGCCUGGCGACGGUUGUCCAGGUUCAAGUGCGUAGGCUUGAGAGUUAGGUAAAUCCGGCUCUCUCUAAGGCUGAGACACGACGUCGAGCACCUACGGGUGUGAAGUCAUUGAUGCCAUGCUUCCAGGAAAAGCCUCUAAGCUUCAGAUUGUAAGGAAUCGUACCCCAAACCGACACAGGUGGUCGGGUAGAGAAUACCAAGGCGCUUGAGAGAACUCGGGUGAAGGAACUAGGCAAAAUGGUACCGUAACUUCGGGAGAAGGUACGCUCUCGACGGUGAAGUCCCUCGCGGAUGGAGCUAUUGAGAGUCGCAGAUACCAGGUGGCUGCAACUGUUUAUUAAAAACACAGCACUGUGCAAAAUCGUAAGAUGACGUAUACGGUGUGACGCCUGCCCGGUGCCGGAAGGUUAAUUGAUGGGGUUAGACUUCGGUCGAAGCUCUUGAUCGAAGCCCCGGUAAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGCGUAAUGAUGGCCACGCUGUCUCCACCCGAGACUCAGUGAAAUUGAAAUCGCUGUGAAGAUGCAGUGUACCCGCGGCUAGACGGAAAGACCCCGUGAACCUUUACUACAGCUUGGCACUGAACAUUGACCCUGUGUUGAUGUUCUAACGUUGACCCCUUAUCGGGGUUGCGGACAGUGCCUGGUGGGUAGUUUGACUGGGGCGGUCUCCUCCCAAAGCGUAACGGAGGAGCACGAAGGUGGGCUAAUCACGGUUCGUGAGGUUAGUGCAAUGGCAUAAGCCCGCUUGACUGCGAGAAUGACAAUUCGAGCAGGUGCGAAAGCAGGUCAUAGUGAUCCGGUGGUUCUGAAUGGAAGGGCCAUCGCUCAACGGAUAAAAGGUACUCCGGGGAUAACAGGCUGAUACCGCCCAAGAGUUCAUAUCGACGGCGGUGUUUGGCACCUCGAUGUCGGCUCAUCACAUCCUGGGGCUGAAGUCGGUCCCAAGGGUAUGGCUGUUCGCCAUUUAAAGUGGUACGCGAGCUGGGUUUAGAACGUCGUGAGACAGUUCGGUCCCUAUCUGCCGUGGGCGUUGGAGAAUUGAAAGGGGCUGCUCCUAGUACGAGAGGACCGGAGUGGACGAACCUCUGGUGUUCGGGUUGUGUCGCCAGACGCAUUGCCCGGUAGCUAAGUUCGGGAUCGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCGAGCCUUGAGAUGAGUUCUCCCUGAUACUUUAAGUAUCCUAAAGGGUUGUCGUAGACUACGACGUUGAUAGGCAGGGUGUGUAAGCGUUGUGAGGCGUUGAGCUAACCUGUACUAAUUGCCCGUGAGGCUUAACC
5S ribosomal RNA b 121 NA UGCUUGGCGACCAUAGCGUUUUGGACCCACCUGACUUCCAUUCCGAACUCAGAAGUGAAACGAAAUAGCGCCGAUGGUAGUGUGGGGUUUCCCCAUGUGAGAGUAGGACAUCGCCAGGCAA
Experimental Data

Method: ELECTRON MICROSCOPY

Deposited Date: 2024-10-29
Deposition Author(s): Bange, G. , Beckert, B. , Koller, T.O. , Lepak, A. , Morici, M. , Raulf, K.F. , Wilson, D.N.