8CVM
Cutibacterium acnes 50s ribosomal subunit with p-site trna and sarecycline bound in the local refined map
PDB DOI: 10.2210/pdb8cvm/pdb
Classification: ANTIBIOTIC Organism(s): Cutibacterium Acnes , Escherichia Coli
Deposited: 2022-05-18 Deposition Author(s): Bunick, C.G. , Devarkar, S.C. , Lomakin, I.B.
Experimental Data Snapshot
Method: ELECTRON MICROSCOPY Resolution: 2.66 Å
Cutibacterium acnes 50s ribosomal subunit with p-site trna and sarecycline bound in the local refined map
Bunick, C.G. , Devarkar, S.C. , Lomakin, I.B.
Primary Citation of Related Structures: 8CVM
| Nucleic Acids / Hybrid | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| Initiator fMet RNA | c | 77 | NA | CGCGGGGUGGAGCAGCCUGGUAGCUCGUCGGGCUCAUAACCCGAAGGUCGUCGGUUCAAAUCCGGCCCCCGCAACCA |
| 23S ribosomal RNA | a | 3086 | NA | GCAAAGUUGUGUAGUGCGAUCGGUGGAUGCCUUGGCACCAAGAGCCGAUGAAGGACGUUGUGACCUGCGAUAAGCCCUGGGGAGUUGGUGAGCGAGCUGUGAUCCGGGGGUGUCCGAAUGGGGAAACCUGGAAUGUCCGGAGUAGUGUCCGGUGGCCCUGCCCUGAAUGUAUAGGGGUGUGGGUGGUAACGCGGGGAAGUGAAACAUCUUAGUACCCGUAGGAAGAGAAAACAAGUGUGAUUCCGUGAGUAGUGGCGAGCGAAAGCGGAGGAGGCUAAACCGUGUGUGUGUUCAAGCCGGCAGGUGUUGCAUGUGCGGGGUUGUGGGGGCCUUGUGGUUCUGCUGCCGCAGGAUUGGCCAGUGAGAAAUGUUGCGUGAAGGUGAAGCGUCUGGGAAGGCGUACCGGAGUGGGUGAGAGUCCUGUAACUGUAAGCGUGGCACUGGUGUGGGGUUGCCCCGAGUAGCGUGGGACUCGUGGAAUUUCGCGUGAAUCUGGCGGGACCACCCGUCAAGCCUAAAUACUCCUUGGUGACCGAUAGUGGAUGAGUACCGUGAGGGAAGGGUGAAAAGUACCCCGGGAGGGGAGUGAAAGAGUUCCUGAAACCGGUCGCAUGCAAGCCGUCAGAGCCUGUGUGGUGAUGGCGUGCCUUUUGAAGAAUGAGCCUGCGAGUUAGUGAUGCGUGGCGAGGUUAACCCGUGGUGGGGGAGUCGUAGCGAAAGCGAGUCCGAUAAGGGCGUGAGUCGCGUGUUCUAGACCCGAAGCGGUGUGAUCUAUCCAUGGCCAGGAUGAAGCGUCGGUAAGACGUCGUGGAGGUCCGAACCCACUUCAGUUGAAAAUGGAGGGGAUGAGUUGUGGAUAGGGGUGAAAGGCCAAUCAAACACCGUGAUAGCUGGUUCUCCCCGAAAUGCAUUUAGGUGCAGCGUUGCGUGGUUCUUGUUGGAGGUAGAGCACUGGAUGGUCUAGGGGGCUUAUCGGCUUACCGAAAUCAGCCAAACUCCGAAUGCUGGCAAGUGUAGCGUGGCAGUGAGACGGCGGGUGAUAAGCUUCGUCGUCGAGAGGGAAACAGCCCAGAUCAUCAGCUAAGGCCCCUAAGUGGUGACUCAGUGGGAAAGGAUGUGGAGUUGCGUAGACAACCAGGAGGUUGGCUUGGAAGCAGCCAUCCUUGAAAGAGUGCGUAAUAGCUCACUGGUCAAGUGAUUCCGCGCCGAUAAUGUAGCGGGGCUUAAGUUAUCCGCCGAAGCUGUGGCAACCUGUGUGGUUGGGUAGGGGAGCGUCGUGUCAGUGGUGAAGCUGCCGGGUGACUGUGUGGUGGAGUUGAUGCGAGUGAGAAUGCAGGCAUGAGUAGCGUGUGACGGGUGGGAAUCCCGUCCGCCGAUUAUCCAAGGGUUCCAGGGUCAAGUUUGUCUGCCCUGGGUGAGUCGGGUCCUAAGGCGAGGCCGACAGGCGUAGUCGAUGGGUAACCAGUUGAUAUUCUGGUACCGGCUUGUCACCGUCCGUGUCGAGGUGUGUGAUGCUAAGCAUGUGAGCUUGUCUUGGGAGUGUUUUUGAUGCUUCUGGGGUGGGUGAGUGUGUGAACCGAUCAUGUAGUAGGCAAGCUGCGGAGGGACGCAGUGAGGUAGCUCAUCCCCGGUGAUGGUUGUCCGGGGCUAAGUGUGUGGACUGUCUGGUAGGUAAAUCCGCUGGGCGUGAAGGUUGAGGCAUGAUGGGGAGCCCAUGGUUGUGGGUGAGUGAGUGAUCCUGUACUGUCGAGAAAAGCUUCGUGAGCGAGGUGGCGGGUCCGCCCGUACCCUAAACCGACACUGGUGGAUAGGUAGAGUAUACCGAGGCGAUCGAGUGAAUCGUGGUGAAGGAACUCGGCAAAAUGCCCCCGUAACUUUGGGAUAAGGGGGACCUGAGCUGUCGUGCACCCGUGCGGUGUGGUGGCGGUGAGGGGCGCAGAGUCCAGGGGGAAACGACUGUUUACCAAAAACACAGGUCCGUGCGAAGUCGUAAGACGAUGUAUACGGACUGACUCCUGCCCGGUGCUGGAAGGUUAAGGGGAACUGUGAGUGUAUGCGUAGCGGUGAACUUAAGCCCCAGUAAACGGCGGUGGUAACXAUAACCAUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAUGGAGUAACGAUUUCCCUACUGUCUCCACCAUGAACUCGGUGAAAUUGCAUUACGAGUAAAGAUGCUCGUUACGCGCAGCAGGACGGAAAGACCCCGGGACCUUUACUAUAGUUUGGUAUUGGUGAUUGGGACGGUUUGUGUAGGAUAGGUGGGAGACGUUGAUGCGGCCACGCUAGUGGUGGUGGAGUCGUUGGUGAAAUACCACUCUGAUUGUUCUGGUUAUCUCACUGUGGACCGUGAUCCGGUUCAAGGACAGUGCCUGAUGGGUAGUUUGACUGGGGCGGUCGCCUCCUAAAGGGUAACGGAGGCGCCCAAAGGUUCCCUCAGCCUGGUUGGUAAUCAGGUGGUGAGUGUAAGUGCACAAGGGGGCUUGACUGUGAGACUGACAGGUCGAGCAGGGACGAAAGUCGGGACUAGUGAUCUGACGGUGGCUUGUGGAUGCGCCGUCACUCAACGGAUAAAAGGUACCCCGGGGAUAACAGGCUGAUCUUGCCCGAGCGCUCAUAGCGACGGCAUGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGGAGUCGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCCCUAUCCGCUGCGCGCGGAGGAAUCUUGAGAAGGGCUGUCUUUAGUACGAGAGGACCGAGACGGACUGACCUCUGGUGUGCCAGUUGUUCUGCCAAGAGCAUGGCUGGUUGGCUACGUCGGGUUGUGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCACGCUUCAAGAUAAGGGUUCCCACAGGAGUGUUCCUGGUAAGGUCCCCGAGAGAUGAUCGGGUUGAUAGGCCAGACGUGGACGCAUCGUAAGGUGUGGAGCUGACUGGUACUAAUAGACCGAGGACUUUCAUUAACA |
| 5S ribosomal RNA | b | 120 | NA | UUUCCGGUGGCCAUAGUGGAAGGGAAACACCCGGUCCCAUUCCGAACCCGGUCGUUAAGCCUUCCAACGCUGAUGGUACUGCACGAGGGAUCGUGUGGGAGAGUAAGACGCUGCCGGAAU |
| Proteins | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Sequence |
| 50S ribosomal protein L17 | M | 187 | Cutibacterium Acnes , Escherichia Coli | MPKPTKGPRLGGSPAHERIILRNLASQLFEHGRVVTTVTKAKRVRPLAEKLINRAKTDTVANRRFVNRTITDRGIVHILFTEIGPRMEGRDGGYTRVTRIGIRKGDNAPMAVIEVISDKVAPKAPASAADAKAQINTATEAKDAEPEAGDAAVEHNAPAEDAAAQAPVADEQEAAEADEKAEEKPEA |
| 50S ribosomal protein L18 | N | 127 | Cutibacterium Acnes , Escherichia Coli | MASTLTVRKSLSDRAKARARRQARGRKKIFGTVERPRMVVTRSSKHVFVQVIDDVAGNTLVSASTMEAELREMSGDKTAKAARVGTIIGERAKAAGITKVVFDKAGNQYHGRIAALADAAREAGLDF |
| 50S ribosomal protein L19 | O | 117 | Cutibacterium Acnes , Escherichia Coli | MSNIIDEIDKASMRDDIPEFRPGDSVKVHVKVVEGSRTRVQVFSGIVISRTGGGVQESFTVRKLSFGTGVERTFPLHSPIIDKIEVDRHGAVRRAKLYYLRGRRGKAAKIKERGSAR |
| 50S ribosomal protein L20 | P | 123 | Cutibacterium Acnes , Escherichia Coli | MARVKRSVNAKKKRREVLDQASGYRGQRSRLYRKAKEQTLHSATYSFRDRRAKKGDFRSLWIQRINAASRAQGMTYNRFINGLKNAGVEVDRKMLAELAVSDINAFNSLVEVAKASQPQNAAA |
| 50S ribosomal protein L21 | Q | 102 | Cutibacterium Acnes , Escherichia Coli | MYAIVRSGGRQHKVAVGDVVEIDKVADEAGSSIELTPLLVVDGESVTSDKDALGKVKVTAEVLGETKGPKIRILKYKNKTGYKKRQGHRQKYTQVKVTGIEG |
| 50S ribosomal protein L22 | R | 153 | Cutibacterium Acnes , Escherichia Coli | MSKTERPSRRAALLGDRPGSYAIARHVRMSASKCRRVINLVRGMDAVDAVTMLKFQPQAAAEPIRKVIASAMANAEQTEGLRADDLYISQAFVDEGITMRRIRPRAKGSASRILKRSAHITVVVEPKEARQARKKAKSGRPAAAAKSETEKGA |
| 50S ribosomal protein L23 | S | 102 | Cutibacterium Acnes , Escherichia Coli | MSELKIRDPRDIILAPVVSEKSYGLLDQNTYTFVVKPTANKTEIKIAIEQIFGVKVTSVNTMNRKGKVRRTRTGVGKRPDTKRAIVTVAEGDRIDIFTGPVA |
| 50S ribosomal protein L24 | T | 122 | Cutibacterium Acnes , Escherichia Coli | MKSLKIKKGDRVKVIAGNDKGAIGEVLSVDPARERVVVEGVNIRKHHRRDMPTPQGGTTKGGIISSEAPIHVSNVQLVTKIDGKDVVTRVGYRRVDVTKRRPDGSEYAAQRSVRYLKKEEAK |
| 50S ribosomal protein L25 | U | 205 | Cutibacterium Acnes , Escherichia Coli | MADIIHLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTENPLLSIEIEGQKPMLALPKDVQRDVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAPGTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIYLGDLKLPEGTSLLGDAEDVAATVAFPETEPVEDEESAGEDAQGESEEKAAKE |
| 50S ribosomal protein bL37 | V | 24 | Cutibacterium Acnes , Escherichia Coli | MGKTGRKRRARRKKGANHGKRPNA |
| 50S ribosomal protein L3 | D | 223 | Cutibacterium Acnes , Escherichia Coli | MTNERTVKGVLGTKLGMTQLWDEHNRLVPVTVIQAGPCVVTQVRTPETDGYSAVQLGYGAVKAKNVTKPEAGHFEKAGVTPRRHLVELRTADASEYTLGQEIAADVFSESDFVDVTGTSKGKGTAGVMKRHGFGGLRATHGVHRKHRSPGSIGGCSTPGKVIKGLRMAGRMGVERVTVQNLQVHSVDAERGIMLVRGAVPGPKGSLLVVRSAAKKAAKNGDAA |
| 50S ribosomal protein L28 | W | 61 | Cutibacterium Acnes , Escherichia Coli | MAAVCDICAKRPGFGHNVPWSKKKTNRRWSPNIQRVRVVENGTHKRMNVCTSCLKAGRVSR |
| 50S ribosomal protein L29 | X | 77 | Cutibacterium Acnes , Escherichia Coli | MPKLSAAELRQLSGEELRNKVRELKEELFGLRFQSATGQLENTARLREVRKDIARVYTVLQERNLNIVDDPDSTKEA |
| 50S ribosomal protein L30 | Y | 60 | Cutibacterium Acnes , Escherichia Coli | MSKLKITQIKSGIATKPNHRETLRSLGLKRIGDTVIKEDRPEFRGMVRTVRHLVTMEEVD |
| 50S ribosomal protein L32 | Z | 63 | Cutibacterium Acnes , Escherichia Coli | MAVPKRKMSRSNTRHRRSQWKTVATKLVTCANPACGEKHLPHTACPSCGGYGPRGDRRQVVEA |
| 50S ribosomal protein L33 | 0 | 56 | Cutibacterium Acnes , Escherichia Coli | MAKKSGDVRPKITLACTECKERNYITKKNRRNNPDRMEMAKFCPRCRKHTAHRETR |
| 50S ribosomal protein L34 | 1 | 44 | Cutibacterium Acnes , Escherichia Coli | MKRTFQPSNRRRARNHGFRSRMSTRAGRSILAARRRKGRVNLSA |
| 50S ribosomal protein L35 | 2 | 68 | Cutibacterium Acnes , Escherichia Coli | MPKMKSHSGTKKRFKVTGSGKVTARKAGKRHLNEHKSSRVTRRLTGETVLSKGEAAKVKKLLAGHPGR |
| 50S ribosomal protein L31 | 4 | 69 | Cutibacterium Acnes , Escherichia Coli | MKQGIHPDYRETTVVCTCGNTFTTRSTSQSGTLNADVCSKCHPFYTGKQKILDAGGRVARFERRYGKKN |
| 50S ribosomal protein L4 | E | 301 | Cutibacterium Acnes , Escherichia Coli | MNETKTIDVLDVKGKKAGSAELPGDLFDVNTNIPLIHQVVVAQLAAARQGTHATKTRGQVSGGGKKPWRQKGTGRARQGSTRAPQWVGGGTVHGPQPRSYAQRTPKKMVGAALRGALSDMARDNRIFVVTSLVDGDKPSTKQAKAVLSGLAELRKVLVVLDRSDEIDWLSVRNLSEVHVLAADQLNTYDVVNARTIVFSQAGLDAFVGARSANTQALSAEPEVPETNVADQHPYGEDSFRGDNPPAGFDIKGNEDSMKFHEPSSPWYGRTIAEVWFRSAAAAEAAGFVNAVKSDSEKEDAK |
| 50S ribosomal protein L36 | 3 | 37 | Cutibacterium Acnes , Escherichia Coli | MKVQPSVKKICDKCKVIRRHGRVMVICDNPRHKQRQG |
| 50S ribosomal protein L5 | F | 210 | Cutibacterium Acnes , Escherichia Coli | MSTDAIAHEMPRLKKQYREQIRAAMQEEFGYRNPMLIPGLEKIVVNMGVGDAAHDSKVMDGAIRDITAITGQKPQVTKARKSIAQFKLREGQPIGCHVTLRGDRMWEFADRLLTLALPRIRDFRGLNSNQFDGKGNYTFGLSEQVMFLEIDQDKIDRIRGMDITFVTTAQTNEEGKALLKHLGFPFKAKDDPKKAKTKRGPAYYAKKKKK |
| 50S ribosomal protein L6 | G | 180 | Cutibacterium Acnes , Escherichia Coli | MSRIGRLPIAVPSGVEVKLDGQYVEVKGPKGTLNFTVREPITVSKNDEGAILVERPDDERENRSLHGLTRTLINNMVIGVTEGYEKKLEIQGVGYRVLSKGPKQLEFNLGFSHPVIVDAPEGITFAVENPTKFSVQGIDKQVVGETAANIRKIRKPEPYKGKGVRYEGENVRRKVGKAGK |
| 50S ribosomal protein L13 | I | 147 | Cutibacterium Acnes , Escherichia Coli | MTTYSPKAGEVQRKWYVIDAEDIVLGRLATTAANLLRGKHKPQYAPHIDTGDFVVVVNASKIALTGKKATDSLRYDHSGRPGGLRVTSIGEMLAKNPRRAVERAVWGMMPKNKLSRQQLKKLKVYGGPEHPHAAQNPQPYEITQIAQ |
| 50S ribosomal protein L14 | J | 122 | Cutibacterium Acnes , Escherichia Coli | MIQQETRLKVADNTGAKELLCIRVLGGSKRRYAYLGDTIVCTVKDAIPGGNVKKGEVVKAVVVRTVKSHRRPDGSYIKFDENAAVLLKGDGEPRGTRIFGPIARELREKKFMRIVSLAPEVI |
| 50S ribosomal protein L15 | K | 146 | Cutibacterium Acnes , Escherichia Coli | MAIELHDLKPAPGAHKAKTRVGRGEGSKGKTAGRGTKGTGARKNVPEFFAGGQMPIHMQAPKLGGFHNPFRTEYQVVNLDKVEALFPKGGKITVDDLVSVGAVRDNELVKVLGTGELTVKVDLVVDAWSKSAQEKIEKAGGSVTKR |
| 50S ribosomal protein L16 | L | 139 | Cutibacterium Acnes , Escherichia Coli | MLIPRRVKYRKQHHPKRTGAAKGGTQLAFGDYGIQATEGGYLTNRQIEAARIAMTRYIKRGGKVWINVYPDRPMTKHPAESRMGSGKGTPEWWIANIKPGRVLFELSGVPEDVAREAMRLAIHKLPMKARFISREGGDN |
Experimental Data
Method: ELECTRON MICROSCOPY
Deposited Date: 2022-05-18 Deposition Author(s): Bunick, C.G. , Devarkar, S.C. , Lomakin, I.B.