5O2R
Cryo-em structure of the proline-rich antimicrobial peptide api137 bound to the terminating ribosome
PDB DOI: 10.2210/pdb5o2r/pdb
Classification: RIBOSOME Organism(s): Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct
Deposited: 2017-05-22 Deposition Author(s): Beckmann, R. , Berninghausen, O. , Graf, M. , Wilson, D.N.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.4 Å
Cryo-em structure of the proline-rich antimicrobial peptide api137 bound to the terminating ribosome
Beckmann, R. , Berninghausen, O. , Graf, M. , Wilson, D.N.
Primary Citation of Related Structures: 5O2R
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S ribosomal RNA | a | 1539 | NA | AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU |
| P-site Ile-tRNA | x | 77 | NA | AGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCA |
| mRNA | 7 | 7 | NA | AUCUAGA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | J | 98 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | RIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISL |
| 30S ribosomal protein S11 | K | 116 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRR |
| 30S ribosomal protein S12 | L | 123 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA |
| 30S ribosomal protein S13 | M | 114 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP |
| 30S ribosomal protein S14 | N | 101 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | AKQSMKAREVKRVALADKYFAKRAELKAIISDVNAASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW |
| 30S ribosomal protein S15 | O | 88 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | P | 82 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | Q | 80 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAV |
| 30S ribosomal protein S18 | R | 65 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | FCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRH |
| 30S ribosomal protein S19 | S | 79 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | RSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYR |
| 30S ribosomal protein S2 | B | 218 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRS |
| 30S ribosomal protein S20 | T | 85 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | NIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S21 | U | 65 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | IKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRT |
| Peptide chain release factor RF1 | V | 242 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | NAFLEVRAGTGGDEAALFAGDLFRMYSRYAEARRWRVEIMSASEGEHGGYKEIIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPDAELPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIHAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGKLDMLIEPIIQEHQAD |
| 50S ribosomal protein L27 | W | 75 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | RNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE |
| 50S ribosomal protein L29 | Y | 63 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| Apidaecin | Z | 14 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | PVYIPRPRPPHPRL |
| 50S ribosomal protein L32 | 0 | 56 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| 50S ribosomal protein L33 | 1 | 50 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAK |
| 50S ribosomal protein L34 | 2 | 46 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| 30S ribosomal protein S3 | C | 206 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEI |
| 50S ribosomal protein L35 | 3 | 64 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| 50S ribosomal protein L36 | 4 | 38 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 50S ribosomal protein L10 | 5 | 131 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MALNLQDKQAIVAEVSEVAKGALSAVVADSRGVTVDKMTELRKAGREAGVYMRVVRNTLLRRAVEGTPFECLKDAFVGPTLIAYSMEHPGAAARLFKEFAKANAKFEVKAAAFEGELIPASQIDRLATLPT |
| 50S ribosomal protein L31 | 6 | 66 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNI |
| 50S ribosomal protein L3 | D | 209 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| 50S ribosomal protein L4 | E | 201 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| 50S ribosomal protein L5 | F | 177 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR |
| 50S ribosomal protein L6 | G | 176 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| 50S ribosomal protein L9 | H | 149 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| 50S ribosomal protein L11 | I | 141 | Escherichia Coli (Strain K12) , Escherichia Coli K-12 , Synthetic Construct | AKKVQAYVKLQVAAGMANPSPPVGPALGQQGVNIMEFCKAFNAKTDSIEKGLPIPVVITVYADRSFTFVTKTPPAAVLLKKAAGIKSGSGKPNKDKVGKISRAQLQEIAQTKAADMTGADIEAMTRSIEGTARSMGLVVED |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2017-05-22 Deposition Author(s): Beckmann, R. , Berninghausen, O. , Graf, M. , Wilson, D.N.