Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound

2025-03-19 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update DATABASE_REFERENCES citation em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation.title _em_admin.last_update DATA_COLLECTION chem_comp_atom chem_comp_bond em_admin _chem_comp_atom.atom_id _chem_comp_atom.pdbx_aromatic_flag _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.value_order _em_admin.last_update RCSB RCSB 2024-06-04 2024-08-21 2024-08-21 2025-03-19 Ortho Dermatologics Canada Cutibacterium acnes 50S ribosomal subunit with Clindamycin bound Lomakin IB Devarkar SC Bunick CG ribosome, clindamycin, acne, ANTIBIOTIC Lomakin IB Devarkar SC Grada A Bunick CG Mechanistic Basis for the Translation Inhibition of Cutibacterium acnes by Clindamycin. J Invest Dermatol. US 144 2553 2561.e3 2024 39122144 doi:10.1016/j.jid.2024.07.013 1523-1747 9c4g FULLOVERLAP 50S subunit with Clindamycin bound 50S subunit with Clindamycin bound 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Cutibacterium acnes 50S ribosomal protein L2 Cutibacterium acnes 0.030309863 1 LEVO MGIRKYKPTTPGRRGSSVSDFVELTRSTPEKSLLVAKPKTGGRNNTGRITTRHIGGGHKQAYRIIDFKRYDKDGVPAKVA HIEYDPNRTARIALLHYADGEKRYIIAPDGVGQGTVVVSGPEADIKPGNNLPLRNIPVGTTVHAVELRPGGGAKMGRSAG ASVQLVAREGKYATVRLPSGEMRMVDIRCRATIGEVGNAEQININWGKAGRNRWKGIRPTVRGVVMNPIDHPHGGGEGRT SGGRHPVSPWGKPEGRTRNKKKASSRLIVRRRKSGKKR A0A2B7JMV5 50S ribosomal protein L3 Cutibacterium acnes 0.023553052999999997 1 LEVO MTNERTVKGVLGTKLGMTQLWDEHNRLVPVTVIQAGPCVVTQVRTPETDGYSAVQLGYGAVKAKNVTKPEAGHFEKAGVT PRRHLVELRTADASEYTLGQEIAADVFSESDFVDVTGTSKGKGTAGVMKRHGFGGLRATHGVHRKHRSPGSIGGCSTPGK VIKGLRMAGRMGVERVTVQNLQVHSVDAERGIMLVRGAVPGPKGSLLVVRSAAKKAAKNGDAA A0A1G9KW65 50S ribosomal protein L4 Cutibacterium acnes 0.032342169999999996 1 LEVO MNETKTIDVLDVKGKKAGSAELPGDLFDVNTNIPLIHQVVVAQLAAARQGTHATKTRGQVSGGGKKPWRQKGTGRARQGS TRAPQWVGGGTVHGPQPRSYAQRTPKKMVGAALRGALSDMARDNRIFVVTSLVDGDKPSTKQAKAVLSGLAELRKVLVVL DRSDEIDWLSVRNLSEVHVLAADQLNTYDVVNARTIVFSQAGLDAFVGARSANTQALSAEPEVPETNVADQHPYGEDSFR GDNPPAGFDIKGNEDSMKFHEPSSPWYGRTIAEVWFRSAAAAEAAGFVNAVKSDSEKEDAK A0A2B7I5M5 50S ribosomal protein L5 Cutibacterium acnes 0.023901756 1 LEVO MSTDAIAHEMPRLKKQYREQIRAAMQEEFGYRNPMLIPGLEKIVVNMGVGDAAHDSKVMDGAIRDITAITGQKPQVTKAR KSIAQFKLREGQPIGCHVTLRGDRMWEFADRLLTLALPRIRDFRGLNSNQFDGKGNYTFGLSEQVMFLEIDQDKIDRIRG MDITFVTTAQTNEEGKALLKHLGFPFKAKDDPKKAKTKRGPAYYAKKKKK A0A3E2DDM1 50S ribosomal protein L6 Cutibacterium acnes 0.019868811 1 LEVO MSRIGRLPIAVPSGVEVKLDGQYVEVKGPKGTLNFTVREPITVSKNDEGAILVERPDDERENRSLHGLTRTLINNMVIGV TEGYEKKLEIQGVGYRVLSKGPKQLEFNLGFSHPVIVDAPEGITFAVENPTKFSVQGIDKQVVGETAANIRKIRKPEPYK GKGVRYEGENVRRKVGKAGK A0A2B7I5S3 50S ribosomal protein L13 Cutibacterium acnes 0.016325824 1 LEVO MTTYSPKAGEVQRKWYVIDAEDIVLGRLATTAANLLRGKHKPQYAPHIDTGDFVVVVNASKIALTGKKATDSLRYDHSGR PGGLRVTSIGEMLAKNPRRAVERAVWGMMPKNKLSRQQLKKLKVYGGPEHPHAAQNPQPYEITQIAQ A0A2B7I6I7 50S ribosomal protein L14 Cutibacterium acnes 0.013503870999999999 1 LEVO MIQQETRLKVADNTGAKELLCIRVLGGSKRRYAYLGDTIVCTVKDAIPGGNVKKGEVVKAVVVRTVKSHRRPDGSYIKFD ENAAVLLKGDGEPRGTRIFGPIARELREKKFMRIVSLAPEVI A0A2B7JMZ8 50S ribosomal protein L15 Cutibacterium acnes 0.015542903 1 LEVO MAIELHDLKPAPGAHKAKTRVGRGEGSKGKTAGRGTKGTGARKNVPEFFAGGQMPIHMQAPKLGGFHNPFRTEYQVVNLD KVEALFPKGGKITVDDLVSVGAVRDNELVKVLGTGELTVKVDLVVDAWSKSAQEKIEKAGGSVTKR A0A2B7IUA0 50S ribosomal protein L16 Cutibacterium acnes 0.015700248 1 LEVO MLIPRRVKYRKQHHPKRTGAAKGGTQLAFGDYGIQATEGGYLTNRQIEAARIAMTRYIKRGGKVWINVYPDRPMTKHPAE SRMGSGKGTPEWWIANIKPGRVLFELSGVPEDVAREAMRLAIHKLPMKARFISREGGDN A0A2B7I5M8 Large ribosomal subunit protein bL17 Cutibacterium acnes 0.020058641 1 LEVO MPKPTKGPRLGGSPAHERIILRNLASQLFEHGRVVTTVTKAKRVRPLAEKLINRAKTDTVANRRFVNRTITDRGIVHILF TEIGPRMEGRDGGYTRVTRIGIRKGDNAPMAVIEVISDKVAPKAPASAADAKAQINTATEAKDAEPEAGDAAVEHNAPAE DAAAQAPVADEQEAAEADEKAEEKPEA A0A8B2VJI7 50S ribosomal protein L18 Cutibacterium acnes 0.013727841 1 LEVO MASTLTVRKSLSDRAKARARRQARGRKKIFGTVERPRMVVTRSSKHVFVQVIDDVAGNTLVSASTMEAELREMSGDKTAK AARVGTIIGERAKAAGITKVVFDKAGNQYHGRIAALADAAREAGLDF A0A2B7JN02 50S ribosomal protein L19 Cutibacterium acnes 0.013106117 1 LEVO MSNIIDEIDKASMRDDIPEFRPGDSVKVHVKVVEGSRTRVQVFSGIVISRTGGGVQESFTVRKLSFGTGVERTFPLHSPI IDKIEVDRHGAVRRAKLYYLRGRRGKAAKIKERGSAR A0A2C6LKT3 50S ribosomal protein L20 Cutibacterium acnes 0.013988012 1 LEVO MARVKRSVNAKKKRREVLDQASGYRGQRSRLYRKAKEQTLHSATYSFRDRRAKKGDFRSLWIQRINAASRAQGMTYNRFI NGLKNAGVEVDRKMLAELAVSDINAFNSLVEVAKASQPQNAAA A0A2B7I6V3 Large ribosomal subunit protein bL21 Cutibacterium acnes 0.011087788 1 LEVO MYAIVRSGGRQHKVAVGDVVEIDKVADEAGSSIELTPLLVVDGESVTSDKDALGKVKVTAEVLGETKGPKIRILKYKNKT GYKKRQGHRQKYTQVKVTGIEG Q6A9I3 50S ribosomal protein L22 Cutibacterium acnes 0.016729471 1 LEVO MSKTERPSRRAALLGDRPGSYAIARHVRMSASKCRRVINLVRGMDAVDAVTMLKFQPQAAAEPIRKVIASAMANAEQTEG LRADDLYISQAFVDEGITMRRIRPRAKGSASRILKRSAHITVVVEPKEARQARKKAKSGRPAAAAKSETEKGA A0A2B7ITY5 50S ribosomal protein L23 Cutibacterium acnes 0.011349219999999998 1 LEVO MSELKIRDPRDIILAPVVSEKSYGLLDQNTYTFVVKPTANKTEIKIAIEQIFGVKVTSVNTMNRKGKVRRTRTGVGKRPD TKRAIVTVAEGDRIDIFTGPVA A0A2C6LEQ5 Large ribosomal subunit protein uL24 Cutibacterium acnes 0.013514626

loop 49-62 is not modeled, no EM density for it

1 LEVO MKSLKIKKGDRVKVIAGNDKGAIGEVLSVDPARERVVVEGVNIRKHHRRDMPTPQGGTTKGGIISSEAPIHVSNVQLVTK IDGKDVVTRVGYRRVDVTKRRPDGSEYAAQRSVRYLKKEEAK Q6A6N7 50S ribosomal protein L25 Cutibacterium acnes 0.022349113 1 LEVO MADIIHLKAEQRTEFGKGAARRIRRDDKVPAVMYGHDHDPIHVTLDGHATLLALRTENPLLSIEIEGQKPMLALPKDVQR DVLKGFVRHVDLLTVRRGEKVDVNVALRITGESAPGTIAMTEFNEIEVQADLLNIPEVIEIDVTGLEAGTTIYLGDLKLP EGTSLLGDAEDVAATVAFPETEPVEDEESAGEDAQGESEEKAAKE A0A2B7IYF8 50S ribosomal protein L27 Cutibacterium acnes 0.009540655 1 LEVO MAHKKGASSSRNGRDSNAQRLGVKRFGGQLVNAGEIIVRQRGTHFHPGDGVGRGGDDTLFALRDGNVEFGTRRGRRVVNV TPVEAPVEA A0A2B7IGT1 50S ribosomal protein L28 Cutibacterium acnes 0.006953212 1 LEVO MAAVCDICAKRPGFGHNVPWSKKKTNRRWSPNIQRVRVVENGTHKRMNVCTSCLKAGRVSR A0A2B7I7B7 50S ribosomal protein L29 Cutibacterium acnes 0.008899072 1 LEVO MPKLSAAELRQLSGEELRNKVRELKEELFGLRFQSATGQLENTARLREVRKDIARVYTVLQERNLNIVDDPDSTKEA A0A2B7JB12 50S ribosomal protein L30 Cutibacterium acnes 0.006932171 1 LEVO MSKLKITQIKSGIATKPNHRETLRSLGLKRIGDTVIKEDRPEFRGMVRTVRHLVTMEEVD A0A2B7I5Y4 50S ribosomal protein L32 Cutibacterium acnes 0.006991127999999999 1 LEVO MAVPKRKMSRSNTRHRRSQWKTVATKLVTCANPACGEKHLPHTACPSCGGYGPRGDRRQVVEA A0A2B7I771 50S ribosomal protein L33 Cutibacterium acnes 0.006725948 1 LEVO MAKKSGDVRPKITLACTECKERNYITKKNRRNNPDRMEMAKFCPRCRKHTAHRETR A0A2C6LJM0 50S ribosomal protein L34 Cutibacterium acnes 0.005185075999999999 1 LEVO MKRTFQPSNRRRARNHGFRSRMSTRAGRSILAARRRKGRVNLSA A0A2B7IDI8 Large ribosomal subunit protein bL35 Cutibacterium acnes 0.007457868 1 LEVO MPKMKSHSGTKKRFKVTGSGKVTARKAGKRHLNEHKSSRVTRRLTGETVLSKGEAAKVKKLLAGHPGR Q6A7V2 50S ribosomal protein L31 Cutibacterium acnes 0.007731770999999999 1 LEVO MKQGIHPDYRETTVVCTCGNTFTTRSTSQSGTLNADVCSKCHPFYTGKQKILDAGGRVARFERRYGKKN A0A2B7JUW7 23S rRNA Cutibacterium acnes 1.002554625 1 GCAAAGUUGUGUAGUGCGAUCGGUGGAUGCCUUGGCACCAAGAGCCGAUGAAGGACGUUGUGACCUGCGAUAAGCCCUGG GGAGUUGGUGAGCGAGCUGUGAUCCGGGGGUGUCCGAAUGGGGAAACCUGGAAUGUCCGGAGUAGUGUCCGGUGGCCCUG CCCUGAAUGUAUAGGGGUGUGGGUGGUAACGCGGGGAAGUGAAACAUCUUAGUACCCGUAGGAAGAGAAAACAAGUGUGA UUCCGUGAGUAGUGGCGAGCGAAAGCGGAGGAGGCUAAACCGUGUGUGUGUUCAAGCCGGCAGGUGUUGCAUGUGCGGGG UUGUGGGGGCCUUGUGGUUCUGCUGCCGCAGGAUUGGCCAGUGAGAAAUGUUGCGUGAAGGUGAAGCGUCUGGGAAGGCG UACCGGAGUGGGUGAGAGUCCUGUAACUGUAAGCGUGGCACUGGUGUGGGGUUGCCCCGAGUAGCGUGGGACUCGUGGAA UUUCGCGUGAAUCUGGCGGGACCACCCGUCAAGCCUAAAUACUCCUUGGUGACCGAUAGUGGAUGAGUACCGUGAGGGAA GGGUGAAAAGUACCCCGGGAGGGGAGUGAAAGAGUUCCUGAAACCGGUCGCAUGCAAGCCGUCAGAGCCUGUGUGGUGAU GGCGUGCCUUUUGAAGAAUGAGCCUGCGAGUUAGUGAUGCGUGGCGAGGUUAACCCGUGGUGGGGGAGUCGUAGCGAAAG CGAGUCCGAUAAGGGCGUGAGUCGCGUGUUCUAGACCCGAAGCGGUGUGAUCUAUCCAUGGCCAGGAUGAAGCGUCGGUA AGACGUCGUGGAGGUCCGAACCCACUUCAGUUGAAAAUGGAGGGGAUGAGUUGUGGAUAGGGGUGAAAGGCCAAUCAAAC ACCGUGAUAGCUGGUUCUCCCCGAAAUGCAUUUAGGUGCAGCGUUGCGUGGUUCUUGUUGGAGGUAGAGCACUGGAUGGU CUAGGGGGCUUAUCGGCUUACCGAAAUCAGCCAAACUCCGAAUGCUGGCAAGUGUAGCGUGGCAGUGAGACGGCGGG (PSU)GAUAAGCUUCGUCGUCGAGAGGGAAACAGCCCAGAUCAUCAGCUAAGGCCCCUAAGUGGUGACUCAGUGGGAAAG GAUGUGGAGUUGCGUAGACAACCAGGAGGUUGGCUUGGAAGCAGCCAUCCUUGAAAGAGUGCGUAAUAGCUCACUGGUCA AGUGAUUCCGCGCCGAUAAUGUAGCGGGGCUUAAGUUAUCCGCCGAAGCUGUGGCAACCUGUGUGGUUGGGUAGGGGAGC GUCGUGUCAGUGGUGAAGCUGCCGGGUGACUGUGUGGUGGAGUUGAUGCGAGUGAGAAUGCAGGCAUGAGUAGCGUGUGA CGGGUGGGAAUCCCGUCCGCCGAUUAUCCAAGGGUUCCAGGGUCAAGUUUGUCUGCCCUGGGUGAGUCGGGUCCUAAGGC GAGGCCGACAGGCGUAGUCGAUGGGUAACCAGUUGAUAUUCUGGUACCGGCUUGUCACCGUCCGUGUCGAGGUGUGUGAU GCUAAGCAUGUGAGCUUGUCUUGGGAGUGUUUUUGAUGCUUCUGGGGUGGGUGAGUGUGUGAACCGAUCAUGUAGUAGGC AAGCUGCGGAGGGACGCAGUGAGGUAGCUCAUCCCCGGUGAUGGUUGUCCGGGGCUAAGUGUGUGGACUGUCUGGUAGGU AAAUCCGCUGGGCGUGAAGGUUGAGGCAUGAUGGGGAGCCCAUGGUUGUGGGUGAGUGAGUGAUCCUGUACUGUCGAGAA AAGCUUCGUGAGCGAGGUGGCGGGUCCGCCCGUACCCUAAACCGACACUGGUGGAUAGGUAGAGUAUACCGAGGCGAUCG AGUGAAUCGUGGUGAAGGAACUCGGCAAAAUGCCCCCGUAACUUUGGGAUAAGGGGGACCUGAGCUGUCGUGCACCCGUG CGGUGUGGUGGCGGUGAGGGGCGCAGAGUCCAGGGGGAAACGACUGUUUACCAAAAACACAGGUCCGUGCGAAGUCGUAA GACGAUGUAUACGGACUGACUCCU(2MG)CCCGGUGCUGGAAGGUUAAGGGGAACUGUGAGUGUAUGCGUAGCGGUGAAC UUAAGCCCCAGUAAACGGCGGUGG(PSU)AAC(3TD)A(PSU)AACCAUCCUAAGGUAGCGAAA(5MU)UCCUUGUCGGG UAAGUUCCGAC(5MC)UGCACGAAUGGAGUAACGAUUUCCCUACUGUCUCCACCAUGAACUCGGUGAAAUUGCAUUACGA GUAAAGAUGCUCGUUACGCGCAGCAGGACGGAAAGACCCCGGGACCUUUACUAUAGUUUGGUAUUGGUGAUUGGGACGGU UUGUGUAGGAUAGGUGGGAGACGUUGAUGCGGCCACGCUAGUGGUGGUGGAGUCGUUGGUGAAAUACCACUCUGAUUGUU CUGGUUAUCUCACUGUGGACCGUGAUCCGGUUCAAGGACAGUGCCUGAUGGGUAGUUUGACUG(OMG)GGCGGUCGCCUC CUAAAGGGUAACGGAGGCGCCCAAAGGUUCCCUCAGCCUGGUUGGUAAUCAGGUGGUGAGUGUAAGUGCACAAGGGGGCU UGACUGUGAGACUGACAGGUCGAGCAGGGACGAAAGUCGGGACUAGUGAUCUGACGGUGGCUUGUGGAUGCGCCGUCACU CAACGGAUAAAAGGUACCCCG(2MG)GGA(H2U)AACAGGC(PSU)GAUCUUGCCCGAGCGCUCAUAGCGACGGCAUGGU UUGGCA(OMC)CUCG(2MA)(PSU)GUCGGCUCGUCGCAUCCUGGGGCUGGAGUCGGUCCCAAGGGUUGGGC(OMU)GUU CGCCCAUUAAAGCGGCACGCGAGC(PSU)GGGUUCAGAACGUCGUGAGACAG(PSU)(PSU)CGGUCCCUAUCCGCUGCG CGCGGAGGAAUCUUGAGAAGGGCUGUCUUUAGUACGAGAGGACCGAGACGGACUGACCUCUGGUGUGCCAGUUGUUCUGC CAAGAGCAUGGCUGGUUGGCUACGUCGGGUUGUGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCACGCUUCAAGAUAAGG GUUCCCACAGGAGUGUUCCUGGUAAGGUCCCCGAGAGAUGAUCGGGUUGAUAGGCCAGACGUGGACGCAUCGUAAGGUGU GGAGCUGACUGGUACUAAUAGACCGAGGACUUUCAUUAACA CP012350.1 5S rRNA Cutibacterium acnes 0.038770055 1 UUUCCGGUGGCCAUAGUGGAAGGGAAACACCCGGUCCCAUUCCGAACCCGGUCGUUAAGCCUUCCAACGCUGAUGGUACU GCACGAGGGAUCGUGUGGGAGAGUAAGACGCUGCCGGAAU CP059593.1 50S ribosomal protein bL37 Cutibacterium acnes 0.002744284 1 LEVO MGKTGRKRRARRKKGANHGKRPNA A0A9Y2YAG1 50S ribosomal protein L36 Cutibacterium acnes 0.004386378999999999 1 LEVO MKVQPSVKKICDKCKVIRRHGRVMVICDNPRHKQRQG A0A2B7JN22 MAGNESIUM ION 2.4305e-05 247 MG ZINC ION 6.5409e-05 4 ZN CLINDAMYCIN 0.000424983 1 CLY water 1.8015e-05 156 HOH singleParticle particle 7.4 ETHANE 100 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 50.0 2.7 0.5 2.8000000000000003 NITROGEN GATAN K3 (6k x 4k) 1.8 38.58 1 2674133 2.53 FSC 0.143 CUT-OFF 283291 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_45185.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 347.19998 347.19998 347.19998 90.0 90.0 90.0 X Y Z -0.35139596 1.1093585 0.00025311203 0.050954327 0.868 0.868 0.868 0.25 AUTHOR ::::EMDATABANK.org::::EMD-45185:::: unsharpened map, flipped FLEXIBLE FIT REAL emd_45185_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 486.08 486.08 486.08 90.0 90.0 90.0 X Y Z -0.77642924 1.4789245 0.0010515508 0.10614811 0.868 0.868 0.868 AUTHOR ::::EMDATABANK.org::::EMD-45185:::: emd_45185_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 560 560 560 0 0 0 560 560 560 486.08 486.08 486.08 90.0 90.0 90.0 X Y Z -0.7944735 1.4512287 0.0010460637 0.1063591 0.868 0.868 0.868 AUTHOR ::::EMDATABANK.org::::EMD-45185::::