5KCS
Cryo-em structure of the escherichia coli 70s ribosome in complex with antibiotic evernimycin, mrna, tetm and p-site trna at 3.9a resolution
PDB DOI: 10.2210/pdb5kcs/pdb
Classification: RIBOSOME Organism(s): Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct
Deposited: 2016-06-06 Deposition Author(s): Arenz, S. , Blanchard, S.C. , Graf, M. , Huter, P. , Juette, M.F. , Nguyen, F. , Polikanov, Y.S. , Wilson, D.N.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 3.9 Å
Cryo-em structure of the escherichia coli 70s ribosome in complex with antibiotic evernimycin, mrna, tetm and p-site trna at 3.9a resolution
Arenz, S. , Blanchard, S.C. , Graf, M. , Huter, P. , Juette, M.F. , Nguyen, F. , Polikanov, Y.S. , Wilson, D.N.
Primary Citation of Related Structures: 5KCS
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S Ribosomal RNA | 1a | 1539 | NA | AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU |
| mRNA | 1v | 60 | NA | AUGGGCAUUUUUAGUAUUUUUGUAAUCAGCACAGUUCAUUAUCAACCAAACAAAAAAUAA |
| P-site tRNA | 1x | 77 | NA | AGGCUUGUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCA |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S10 | 1J | 103 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG |
| 30S ribosomal protein S11 | 1K | 129 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAKAPIRARKRVRKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV |
| 30S ribosomal protein S14 | 1N | 101 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAKQSMKAREVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW |
| 30S ribosomal protein S15 | 1O | 89 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MSLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | 1P | 82 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | 1Q | 84 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MTDKIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAVL |
| 30S ribosomal protein S18 | 1R | 75 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MARYFRRRKFCRFTAEGVQEIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRHQ |
| 30S ribosomal protein S19 | 1S | 92 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MPRSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHAADKKAKKK |
| 30S ribosomal protein S20 | 1T | 87 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S21 | 1U | 71 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MPVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHAKKLARENARRTRLY |
| 30S ribosomal protein S2 | 1B | 241 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MATVSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQDLASQAEESFVEAE |
| Tetracycline resistance protein TetM from transposon Tn916 | 1W | 639 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MKIINIGVLAHVDAGKTTLTESLLYNSGAITELGSVDKGTTRTDNTLLERQRGITIQTGITSFQWENTKVNIIDTPGHMDFLAEVYRSLSVLDGAILLISAKDGVQAQTRILFHALRKMGIPTIFFINKIDQNGIDLSTVYQDIKEKLSAEIVIKQKVELYPNVCVTNFTESEQWDTVIEGNDDLLEKYMSGKSLEALELEQEESIRFQNCSLFPLYHGSAKSNIGIDNLIEVITNKFYSSTHRGPSELCGNVFKIEYTKKRQRLAYIRLYSGVLHLRDSVRVSEKEKIKVTEMYTSINGELCKIDRAYSGEIVILQNEFLKLNSVLGDTKLLPQRKKIENPHPLLQTTVEPSKPEQREMLLDALLEISDSDPLLRYYVDSTTHEIILSFLGKVQMEVISALLQEKYHVEIEITEPTVIYMERPLKNAEYTIHIEVPPNPFWASIGLSVSPLPLGSGMQYESSVSLGYLNQSFQNAVMEGIRYGCEQGLYGWNVTDCKICFKYGLYYSPVSTPADFRMLAPIVLEQVLKKAGTELLEPYLSFKIYAPQEYLSRAYNDAPKYCANIVDTQLKNNEVILSGEIPARCIQEYRSDLTFFTNGRSVCLTELKGYHVTTGEPVCQPRRPNSRIDKVRYMFNKIT |
| 50S ribosomal protein L24 | 1Y | 104 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAAKIRRDDEVIVLTGKDKGKRGKVKNVLSSGKVIVEGINLVKKHQKPVPALNQPGGIVEKEAAIQVSNVAIFNAATGKADRVGFRFEDGKKVRFFKSNSETIK |
| 50S ribosomal protein L25 | 1Z | 94 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA |
| 50S ribosomal protein L27 | 10 | 85 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAHKKAGGSTRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE |
| 50S ribosomal protein L28 | 11 | 78 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MSRVCQVTGKRPVTGNNRSHALNATKRRFLPNLHSHRFWVESEKRFVTLRVSAKGMRVIDKKGIDTVLAELRARGEKY |
| 50S ribosomal protein L29 | 12 | 63 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MKAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| 50S ribosomal protein L30 | 13 | 59 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAIRGMINAVSFMVKVEE |
| 50S ribosomal protein L31 | 14 | 70 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNIPGSK |
| 30S ribosomal protein S4 | 1D | 206 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MARYLGPKLKLSRREGTDLFLKSGVRAIDTKCKIEQAPGQHGARKPRLSDYGVQLREKQKVRRIYGVLERQFRNYYKEAARLKGNTGENLLALLEGRLDNVVYRMGFGATRAEARQLVSHKAIMVNGRVVNIASYQVSPNDVVSIREKAKKQSRVKAALELAEQREKPTWLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK |
| 50S ribosomal protein L32 | 15 | 57 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| 50S ribosomal protein L33 | 16 | 55 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAKGIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKIK |
| 50S ribosomal protein L34 | 17 | 46 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| 50S ribosomal protein L35 | 18 | 65 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MPKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| 50S ribosomal protein L36 | 19 | 38 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 30S ribosomal protein S3 | 1C | 233 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MGQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEILGGMAAVEQPEKPAAQPKKQQRKGRK |
| 50S ribosomal protein L3 | 1E | 209 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| 50S ribosomal protein L4 | 1F | 201 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| 50S ribosomal protein L5 | 1G | 179 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MAKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFRK |
| 50S ribosomal protein L6 | 1H | 177 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| 50S ribosomal protein L9 | 1I | 149 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| 50S ribosomal protein L7/L12 | 1L | 121 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MSITKDQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVAVAAGPVEAAEEKTEFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK |
| 30S ribosomal protein S13 | 1M | 118 | Enterococcus Faecalis , Escherichia Coli (Strain K12) , Synthetic Construct | MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKPIKK |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2016-06-06 Deposition Author(s): Arenz, S. , Blanchard, S.C. , Graf, M. , Huter, P. , Juette, M.F. , Nguyen, F. , Polikanov, Y.S. , Wilson, D.N.