7B5K
E. coli 70s containing suppressor trna in the a-site stabilized by a negamycin analogue and p-site trna-nascent chain.
PDB DOI: 10.2210/pdb7b5k/pdb
Classification: RIBOSOME Organism(s): Escherichia Coli K-12 , Synthetic Construct
Deposited: 2020-12-03 Deposition Author(s): Albers, S. , Beckert, B. , Ignatova, Z. , Matthies, M. , Riedner, M. , Sanyal, S. , Schuster, R. , Seuring, C. , Torda, A. , Wilson, N.D.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.9 Å
E. coli 70s containing suppressor trna in the a-site stabilized by a negamycin analogue and p-site trna-nascent chain.
Albers, S. , Beckert, B. , Ignatova, Z. , Matthies, M. , Riedner, M. , Sanyal, S. , Schuster, R. , Seuring, C. , Torda, A. , Wilson, N.D.
Primary Citation of Related Structures: 7B5K
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 16S rRNA | a | 1533 | NA | AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCCGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUC |
| P-site Isoleucine tRNA (77-MER) | x | 77 | NA | AGGCUUAUAGCUCAGGUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGGUGGUUCAAGUCCACUCAGGCCUACCA |
| atRNA synthetic Stop tRNA (76-MER) | z | 76 | NA | GGGGUGGUGGCUCAGAAGGGAGAGCAGCGGCCUUCAGAGCCGCGAGACGGGGGUUCGAUUCCCCUCCGCUCCACCA |
| E-site val tRNA (76-MER) | 9 | 76 | NA | GGGUGAUUAGCUCAGCUGGGAGAGCACCUCCCUUACAAGGAGGUGGUCGGCGGUUCGAUCCCGUCAUCACCCACCA |
| mRNA | 6 | 11 | NA | GUAAUCUGAAC |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 30S ribosomal protein S11 | K | 117 | Escherichia Coli K-12 , Synthetic Construct | RKQVSDGVAHIHASFNNTIVTITDRQGNALGWATAGGSGFRGSRKSTPFAAQVAAERCADAVKEYGIKNLEVMVKGPGPGRESTIRALNAAGFRITNITDVTPIPHNGCRPPKKRRV |
| 30S ribosomal protein S12 | L | 123 | Escherichia Coli K-12 , Synthetic Construct | ATVNQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKXLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA |
| 30S ribosomal protein S13 | M | 114 | Escherichia Coli K-12 , Synthetic Construct | ARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEVAKFVVEGDLRREISMSIKRLMDLGCYRGLRHRRGLPVRGQRTKTNARTRKGPRKP |
| 30S ribosomal protein S14 | N | 101 | Escherichia Coli K-12 , Synthetic Construct | AKQSMKAREVKRVALADKYFAKRAELKAIISDVNAASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGRPHGFLRKFGLSRIKVREAAMRGEIPGLKKASW |
| 30S ribosomal protein S15 | O | 88 | Escherichia Coli K-12 , Synthetic Construct | SLSTEATAKIVSEFGRDANDTGSTEVQVALLTAQINHLQGHFAEHKKDHHSRRGLLRMVSQRRKLLDYLKRKDVARYTQLIERLGLRR |
| 30S ribosomal protein S16 | P | 82 | Escherichia Coli K-12 , Synthetic Construct | MVTIRLARHGAKKRPFYQVVVADSRNARNGRFIERVGFFNPIASEKEEGTRLDLDRIAHWVGQGATISDRVAALIKEVNKAA |
| 30S ribosomal protein S17 | Q | 80 | Escherichia Coli K-12 , Synthetic Construct | KIRTLQGRVVSDKMEKSIVVAIERFVKHPIYGKFIKRTTKLHVHDENNECGIGDVVEIRECRPLSKTKSWTLVRVVEKAV |
| 30S ribosomal protein S18 | R | 55 | Escherichia Coli K-12 , Synthetic Construct | EIDYKDIATLKNYITESGKIVPSRITGTRAKYQRQLARAIKRARYLSLLPYTDRH |
| 30S ribosomal protein S19 | S | 82 | Escherichia Coli K-12 , Synthetic Construct | RSLKKGPFIDLHLLKKVEKAVESGDKKPLRTWSRRSTIFPNMIGLTIAVHNGRQHVPVFVTDEMVGHKLGEFAPTRTYRGHA |
| 30S ribosomal protein S20 | T | 86 | Escherichia Coli K-12 , Synthetic Construct | ANIKSAKKRAIQSEKARKHNASRRSMMRTFIKKVYAAIEAGDKAAAQKAFNEMQPIVDRQAAKGLIHKNKAARHKANLTAQINKLA |
| 30S ribosomal protein S2 | B | 224 | Escherichia Coli K-12 , Synthetic Construct | VSMRDMLKAGVHFGHQTRYWNPKMKPFIFGARNKVHIINLEKTVPMFNEALAELNKIASRKGKILFVGTKRAASEAVKDAALSCDQFFVNHRWLGGMLTNWKTVRQSIKRLKDLETQSQDGTFDKLTKKEALMRTRELEKLENSLGGIKDMGGLPDALFVIDADHEHIAIKEANNLGIPVFAIVDTNSDPDGVDFVIPGNDDAIRAVTLYLGAVAATVREGRSQ |
| 30S ribosomal protein S21 | U | 56 | Escherichia Coli K-12 , Synthetic Construct | PVIKVRENEPFDVALRRFKRSCEKAGVLAEVRRREFYEKPTTERKRAKASAVKRHA |
| ermC Nacent chain | V | 8 | Escherichia Coli K-12 , Synthetic Construct | GIFSIFVI |
| 50S ribosomal protein L27 | W | 76 | Escherichia Coli K-12 , Synthetic Construct | TRNGRDSEAKRLGVKRFGGESVLAGSIIVRQRGTKFHAGANVGCGRDHTLFAKADGKVKFEVKGPKNRKFISIEAE |
| 50S ribosomal protein L29 | Y | 62 | Escherichia Coli K-12 , Synthetic Construct | KAKELREKSVEELNTELLNLLREQFNLRMQAASGQLQQSHLLKQVRRDVARVKTLLNEKAGA |
| 50S ribosomal protein L32 | 0 | 56 | Escherichia Coli K-12 , Synthetic Construct | AVQQNKPTRSKRGMRRSHDALTAVTSLSVDKTSGEKHLRHHITADGYYRGRKVIAK |
| 50S ribosomal protein L33 | 1 | 51 | Escherichia Coli K-12 , Synthetic Construct | GIREKIKLVSSAGTGHFYTTTKNKRTKPEKLELKKFDPVVRQHVIYKEAKI |
| 50S ribosomal protein L34 | 2 | 46 | Escherichia Coli K-12 , Synthetic Construct | MKRTFQPSVLKRNRSHGFRARMATKNGRQVLARRRAKGRARLTVSK |
| 50S ribosomal protein L35 | 3 | 64 | Escherichia Coli K-12 , Synthetic Construct | PKIKTVRGAAKRFKKTGKGGFKHKHANLRHILTKKATKRKRHLRPKAMVSKGDLGLVIACLPYA |
| 30S ribosomal protein S3 | C | 206 | Escherichia Coli K-12 , Synthetic Construct | GQKVHPNGIRLGIVKPWNSTWFANTKEFADNLDSDFKVRQYLTKELAKASVSRIVIERPAKSIRVTIHTARPGIVIGKKGEDVEKLRKVVADIAGVPAQINIAEVRKPELDAKLVADSITSQLERRVMFRRAMKRAVQNAMRLGAKGIKVEVSGRLGGAEIARTEWYREGRVPLHTLRADIDYNTSEAHTTYGVIGVKVWIFKGEI |
| 50S ribosomal protein L36 | 4 | 38 | Escherichia Coli K-12 , Synthetic Construct | MKVRASVKKLCRNCKIVKRDGVIRVICSAEPKHKQRQG |
| 50S ribosomal protein L31 | 5 | 66 | Escherichia Coli K-12 , Synthetic Construct | MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFNI |
| 50S ribosomal protein L3 | D | 209 | Escherichia Coli K-12 , Synthetic Construct | MIGLVGKKVGMTRIFTEDGVSIPVTVIEVEANRVTQVKDLANDGYRAIQVTTGAKKANRVTKPEAGHFAKAGVEAGRGLWEFRLAEGEEFTVGQSISVELFADVKKVDVTGTSKGKGFAGTVKRWNFRTQDATHGNSLSHRVPGSIGQNQTPGKVFKGKKMAGQMGNERVTVQSLDVVRVDAERNLLLVKGAVPGATGSDLIVKPAVKA |
| 50S ribosomal protein L4 | E | 201 | Escherichia Coli K-12 , Synthetic Construct | MELVLKDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGTGRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFSVEAPKTKLLAQKLKDMALEDVLIITGELDENLFLAARNLHKVDVRDATGIDPVSLIAFDKVVMTADAVKQVEEMLA |
| 50S ribosomal protein L5 | F | 177 | Escherichia Coli K-12 , Synthetic Construct | AKLHDYYKDEVVKKLMTEFNYNSVMQVPRVEKITLNMGVGEAIADKKLLDNAAADLAAISGQKPLITKARKSVAGFKIRQGYPIGCKVTLRGERMWEFFERLITIAVPRIRDFRGLSAKSFDGRGNYSMGVREQIIFPEIDYDKVDRVRGLDITITTTAKSDEEGRALLAAFDFPFR |
| 50S ribosomal protein L6 | G | 176 | Escherichia Coli K-12 , Synthetic Construct | SRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK |
| 50S ribosomal protein L9 | H | 149 | Escherichia Coli K-12 , Synthetic Construct | MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE |
| 30S ribosomal protein S9 | I | 127 | Escherichia Coli K-12 , Synthetic Construct | NQYYGTGRRKSSAARVFIKPGNGKIVINQRSLEQYFGRETARMVVRQPLELVDMVEKLDLYITVKGGGISGQAGAIRHGITRALMEYDESLRSELRKAGFVTRDARQVERKKVGLRKARRRPQFSKR |
| 50S ribosomal protein L13 | J | 142 | Escherichia Coli K-12 , Synthetic Construct | MKTFTAKPETVKRDWYVVDATGKTLGRLATELARRLRGKHKAEYTPHVDTGDYIIVLNADKVAVTGNKRTDKVYYHHTGHIGGIKQATFEEMIARRPERVIEIAVKGMLPKGPLGRAMFRKLKVYAGNEHNHAAQQPQVLDI |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2020-12-03 Deposition Author(s): Albers, S. , Beckert, B. , Ignatova, Z. , Matthies, M. , Riedner, M. , Sanyal, S. , Schuster, R. , Seuring, C. , Torda, A. , Wilson, N.D.