7S1I

Wild-type Escherichia coli stalled ribosome with antibiotic radezolid

  • Classification: RIBOSOME
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-09-02 Released: 2022-03-02 
  • Deposition Author(s): Young, I.D., Stojkovic, V., Tsai, K., Lee, D.J., Fraser, J.S., Galonic Fujimori, D.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Other government, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Simons Foundation, W. M. Keck Foundation, Other private, National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics.

Tsai, K., Stojkovic, V., Lee, D.J., Young, I.D., Szal, T., Klepacki, D., Vazquez-Laslop, N., Mankin, A.S., Fraser, J.S., Fujimori, D.G.

(2022) Nat Struct Mol Biol 29: 162-171

  • DOI: 10.1038/s41594-022-00723-9
  • Primary Citation of Related Structures:  
    7S1G, 7S1H, 7S1I, 7S1J, 7S1K

  • PubMed Abstract: 

    • The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain ...

    The antibiotic linezolid, the first clinically approved member of the oxazolidinone class, inhibits translation of bacterial ribosomes by binding to the peptidyl transferase center. Recent work has demonstrated that linezolid does not inhibit peptide bond formation at all sequences but rather acts in a context-specific manner, namely when alanine occupies the penultimate position of the nascent chain. However, the molecular basis for context-specificity has not been elucidated. Here we show that the second-generation oxazolidinone radezolid also induces stalling with a penultimate alanine, and we determine high-resolution cryo-EM structures of linezolid- and radezolid-stalled ribosome complexes to explain their mechanism of action. These structures reveal that the alanine side chain fits within a small hydrophobic crevice created by oxazolidinone, resulting in improved ribosome binding. Modification of the ribosome by the antibiotic resistance enzyme Cfr disrupts stalling due to repositioning of the modified nucleotide. Together, our findings provide molecular understanding for the context-specificity of oxazolidinones.

    Organizational Affiliation: 

    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA. Danica.Fujimori@ucsf.edu.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19A [auth 1]92Escherichia coliMutation(s): 0 
UniProt
Find proteins for S1EA57 (Escherichia coli KTE73)
Explore S1EA57 
Go to UniProtKB:  S1EA57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS1EA57
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20B [auth 2]87Escherichia coliMutation(s): 0 
Gene Names: 
rpsT, A2F99_000113, A5U30_000450, A6592_03780, A8499_002827, A8X14_001145, A9X72_21175, AAG43_001657, AAG80_000282, AAG81_003492, ACN68_05610, ACN81_29300, ACU57_08035, AM464_16860, APX88_15255, AT335_001248, AT845_001354, AW118_10515, AW119_13135, AWP47_04800, B6R12_004523, B6R15_000372, B6R31_002612, B6R48_000869, B6R87_000870, BANRA_00498, BANRA_00987, BEA19_04245, BER14_08565, BF481_004322, BG944_002014, BHS81_26325, BJI68_23170, BJJ90_22105, BK292_12910, BK383_13810, BMC79_000180, BMT49_01400, BMT50_04750, BMT91_02105, BN17_44451, BO068_001988, BO178_002094, BOH76_19895, BON63_03890, BON64_08480, BON65_08640, BON66_13640, BON67_10765, BON68_06115, BON69_07945, BON70_02895, BON71_00180, BON72_08605, BON73_04535, BON74_01795, BON75_16375, BON76_14695, BON77_21145, BON78_07485, BON79_16465, BON80_15535, BON81_06000, BON82_12405, BON83_25630, BON84_03175, BON86_13820, BON87_17510, BON88_10955, BON89_27395, BON90_21500, BON91_07775, BON92_01985, BON93_19710, BON94_26365, BON95_00690, BON96_04625, BON97_15465, BON98_07785, BR158_000647, BSR05_19870, BTQ06_20830, BvCmsF30A_01100, BvCmsHHP019_02949, BvCmsHHP056_00611, BvCmsKKP036_02890, BvCmsKKP061_01774, BvCmsKSNP073_00873, BVL39_02950, BXT93_08445, BZL69_04225, C2121_001348, C2M16_10025, C2U48_10405, C3F40_13025, C5N07_07795, C5Y87_11700, C9114_07750, C9160_20885, C9E67_26000, C9Z68_04045, CA593_03645, CCS08_23355, CCV12_002145, CCV24_000878, CDC27_23895, CDL36_07135, CDL37_17225, CG831_004095, CIG67_13240, CO706_22290, CR538_21410, CR539_04110, CSE52_002355, CWS33_08845, CX692_000113, CX693_000113, CX694_001137, CX699_000113, CXJ73_000871, CY655_00115, CYM75_003131, D0X26_10200, D1912_24535, D1H34_001329, D3822_02215, D3C88_27595, D3G36_11455, D3Y67_20370, D4U49_01065, D9D43_03045, D9D77_06665, D9E34_01855, D9E49_02920, D9H94_05850, D9J03_00920, D9J61_10145, DAH17_02290, DAH18_06080, DAH19_13685, DAH20_13050, DAH21_15015, DAH22_04440, DAH23_11995, DAH24_12065, DAH25_11940, DAH26_12005, DAH27_12615, DAH28_04450, DAH29_13920, DAH30_11385, DAH31_14840, DAH32_09535, DAH33_15070, DAH35_06035, DAH36_12665, DAH37_06000, DAH38_13530, DAH40_15185, DAH41_08225, DAH42_00770, DAH43_03235, DAH45_05455, DAH46_03425, DAH47_00965, DAH48_02980, DAH49_03235, DAH50_07815, DD762_00305, DEN86_04855, DEN87_15325, DEN88_20025, DEN89_19835, DEN90_18175, DEN91_24865, DEN92_24465, DEN93_19105, DEN94_15330, DEN95_11390, DEN96_05415, DEN97_05200, DEN98_05205, DEN99_02340, DEO00_04415, DEO01_05230, DEO02_10310, DEO03_07835, DEO04_16330, DEO05_16190, DEO06_15385, DEO07_15510, DEO08_03605, DEO09_16055, DEO10_16315, DEO11_16195, DEO12_14610, DEO13_09415, DEO14_12015, DEO15_09195, DEO17_20360, DEO18_02615, DEO19_04985, DEO20_18945, DIV22_05480, DKP82_13500, DM870_18735, DN627_12515, DNQ45_08590, DNX30_03070, DRW19_05700, DS732_05000, DTL43_06695, DTL90_19710, DTM45_11855, DU321_02915, DXT69_02265, DXT70_21770, DXT71_01135, DXT73_11895, E0I42_21365, E2112_01985, E2113_14180, E2114_00490, E2115_07450, E2116_06175, E2117_06235, E2118_04395, E2119_08150, E2120_09485, E2121_11355, E2122_03730, E2123_06295, E2124_05915, E2125_15540, E2127_05190, E2128_11160, E2129_03585, E2130_09610, E2131_02760, E2132_05195, E2133_02915, E2134_11250, E2135_03870, E2136_04540, E2646_16925, E3N34_04640, E3O05_10715, E4K51_06530, E4T14_03055, E4T84_09660, E5M02_03645, E5P22_20740, E5P23_03985, E5P24_22430, E5P25_23540, E5P26_22885, E5P27_22000, E5P28_23935, E5P29_08905, E5P30_07980, E5P31_04320, E5P32_13400, E5P33_19440, E5P34_22355, E5P35_17395, E5P36_17725, E5P37_11280, E5P39_14525, E5P40_16580, E5P41_21940, E5P42_14160, E5P43_10240, E5P44_10590, E5P45_09795, E5P46_22950, E5P47_12285, E5P48_21440, E5P49_12270, E5P50_01735, E5P51_05170, E5P52_15535, E5S34_13265, E5S35_00880, E5S36_10385, E5S37_12575, E5S38_08300, E5S39_14180, E5S42_10600, E5S43_02510, E5S44_08735, E5S45_05575, E5S46_04750, E5S47_11595, E5S48_15200, E5S51_07540, E5S52_10245, E5S53_11375, E5S54_13385, E5S55_10350, E5S56_10845, E5S57_07990, E5S58_06350, E5S59_11965, E5S61_04640, E5S62_07060, EA239_16620, EA435_08595, EAI46_14690, EAN77_10175, EAX79_06270, EBP16_09825, EC95NR1_04202, ECs0026, ED648_00915, EHD79_22715, EI021_05080, EIA08_05570, EIZ93_24750, EKI52_11270, EL79_3849, EL80_3795, ELT16_08355, ELT17_00515, ELT20_03730, ELT21_05220, ELT22_08090, ELT23_12935, ELT24_04685, ELT25_07375, ELT26_06315, ELT27_05210, ELT28_10155, ELT29_02175, ELT30_07755, ELT31_07930, ELT32_03975, ELT33_16630, ELT34_06350, ELT35_06030, ELT36_00620, ELT38_14210, ELT39_06645, ELT40_02920, ELT41_01235, ELT44_07030, ELT45_09225, ELT46_10830, ELT48_11370, ELT49_10205, ELT50_05685, ELT51_06575, ELT52_04880, ELT54_15285, ELT55_10740, ELT56_05705, ELT58_07905, ELT59_07760, ELT60_05445, ELT61_08610, ELT63_03970, ELT72_06500, ELU07_00295, ELU82_14850, ELU83_07145, ELU85_11930, ELU88_13575, ELU89_24045, ELU90_04375, ELU91_05095, ELU94_05965, ELU95_06505, ELU96_07380, ELU97_08695, ELU98_15735, ELU99_06340, ELV00_15180, ELV01_06645, ELV02_12305, ELV03_11865, ELV04_05735, ELV05_10940, ELV07_03785, ELV08_21540, ELV09_01875, ELV10_23900, ELV11_08105, ELV12_09080, ELV13_02380, ELV15_11805, ELV16_15075, ELV20_02425, ELV21_12930, ELV22_04360, ELV23_05820, ELV26_09090, ELV28_04920, ELV29_22450, ELV40_00185, ELX48_03325, ELX61_08320, ELX66_05990, ELX68_06750, ELX69_08980, ELX76_13825, ELX79_04520, ELX85_13275, ELX96_18205, ELY02_14525, ELY31_09850, ELY32_07720, ELY36_05835, ELY39_00605, ELY41_07000, ELY48_06715, EPS76_15825, ERS085406_00416, ERS085411_00201, ERS139208_01085, EWK56_14125, ExPECSC038_04138, EXX13_04575, EYV17_17815, EYV18_04750, EYX47_11270, F0L67_09855, F2N31_00890, F3N40_06625, F7F11_02830, F9B07_04255, F9S83_03010, F9V22_05475, F9V24_01495, F9X20_08620, FDM60_06600, FE587_08420, FEJ01_07985, FEL34_01040, FFF58_06910, FGG80_06415, FHD44_13430, FJQ51_00910, FKO60_25310, FOI11_013580, FOI11_22100, FPI65_00060, FQF29_02260, FTV90_08385, FTV92_14095, FTV93_14405, FV293_03630, FVB16_23965, FWK02_19890, FY127_05660, FZC17_12070, FZN31_20675, G3565_16585, G3813_000663, G4A38_11000, G5603_15185, G9448_10840, GAJ26_10375, GF147_14040, GF199_00915, GF698_06965, GF699_05480, GFY34_15075, GGB84_001424, GIB53_23825, GJ11_00120, GKF89_01750, GNZ05_10535, GP711_08775, GQM04_03640, GQM09_06380, GQM13_11900, GQW07_13370, GQW68_00905, GQW80_07515, GRC73_18055, GRO95_10250, GRW05_18565, GRW57_19055, GSY44_00915, GTP88_06230, GUC01_17160, GUI33_00965, H0O72_17735, H6Y26_001855, HHH44_001269, HI055_000925, HIE29_002940, HIN64_000697, HIO80_003416, HJQ60_000838, HJS37_001773, HJU54_003283, HKA49_001794, HL563_03475, HL601_06950, HLV18_10075, HLZ50_14320, HmCms169_00205, HMJ82_00920, HMU06_10850, HMV95_05330, HMW38_14705, HNC36_14195, HNC59_09690, HNC66_12420, HNC99_08585, HND12_09605, HV109_20105, HV209_00820, HV209_22380, HVV39_16845, HVW04_10975, HVW19_14235, HVW43_12510, HVX16_21985, HVX31_16960, HVY77_21905, HVZ30_17585, HVZ71_21140, HX136_21355, I6H00_14880, I6H02_17860, IA00_000183, IFB95_000706, IH768_05210, IH772_13695, IT029_004745, J0541_002476, J4S20_002230, J5U05_003239, JE86ST02C_00220, JE86ST05C_00220, JFD_01111, JNP96_04295, NCTC10082_01545, NCTC10089_04234, NCTC10418_06301, NCTC10429_04410, NCTC10764_05953, NCTC10767_03791, NCTC10865_05258, NCTC10974_04789, NCTC11112_03207, NCTC11126_03412, NCTC11181_01521, NCTC11341_03418, NCTC12950_04579, NCTC13127_05620, NCTC13148_04985, NCTC13216_02575, NCTC4450_01210, NCTC7922_05631, NCTC7927_04659, NCTC8008_03818, NCTC8009_07557, NCTC8179_01182, NCTC8333_04915, NCTC8450_00932, NCTC8500_04735, NCTC8621_04353, NCTC8622_02456, NCTC8959_04686, NCTC8960_01711, NCTC8985_03329, NCTC9036_04171, NCTC9037_04333, NCTC9044_02991, NCTC9045_04893, NCTC9075_05681, NCTC9077_05304, NCTC9111_04410, NCTC9702_04945, NCTC9706_01568, NCTC9775_02487, NCTC9777_00624, NCTC9962_05928, ND22_003492, RG28_04645, SAMEA3472044_01892, SAMEA3472056_01123, SAMEA3472147_00231, SAMEA3751407_02526, SAMEA3753106_01651, TUM18780_37490, WP4S18E07_38390, WR15_01590

UniProt
Find proteins for C3TRH7 (Escherichia coli)
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UniProt GroupC3TRH7
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21C [auth 3]71Escherichia coliMutation(s): 0 
UniProt
Find proteins for A0A0E2L2J1 (Escherichia coli (strain UMEA 3162-1))
Explore A0A0E2L2J1 
Go to UniProtKB:  A0A0E2L2J1
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UniProt GroupA0A0E2L2J1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2G [auth D]241Escherichia coliMutation(s): 0 
Gene Names: 
rpsB, A2F99_001367, A5U30_000304, A6592_02990, A8499_001874, A8X14_001297, AAG43_001513, AAG80_000434, AAG81_004372, AAS29_001208, AM464_17645, APX88_24825, AT335_002551, AT845_002206, AW118_17855, AW119_13910, AWP47_05585, B6R12_000948, B6R15_000228, B6R31_002468, B6R48_000725, B6R87_000726, BEA19_03470, BER14_07785, BF481_003689, BJI68_15640, BJJ90_21360, BK383_20240, BMC79_000033, BMT49_02175, BMT91_01365, BO068_002859, BO178_001944, BOB65_001496, BON65_09430, BON66_02955, BON73_05315, BON74_02575, BON75_17145, BON77_21925, BON78_08295, BON79_15655, BON80_16315, BON81_06770, BON82_14460, BON83_24855, BON84_04025, BON86_04410, BON87_26695, BON88_11785, BON89_11025, BON90_22335, BON91_06960, BON92_02750, BON93_03940, BON96_17215, BON98_18185, BR158_000500, BR331_02985, BRV34_001356, BRV41_001378, BSR05_12115, BvCmsHHP019_00044, BvCmsHHP056_04094, BvCmsKKP036_03788, BXT93_00705, BZL69_20205, C2121_002936, C2M16_10795, C2U48_09610, C3F40_12245, C5N07_08575, C5Y87_12570, C9E67_25210, C9Z68_04785, CA593_02870, CCV12_002000, CCV24_000720, CDC27_24690, CDL36_07905, CDL37_07245, CG831_000820, CIG67_16575, CR539_04935, CSE52_002183, CX692_001437, CX693_001437, CX694_000987, CX699_001375, CXJ73_002503, CY655_00895, CYM75_004174, D0X26_09420, D1912_13690, D1H34_004216, D3822_17335, D3G36_16675, D3Y67_16405, D4U49_05950, D9D43_02305, D9E34_01105, D9E49_02145, D9J03_00165, D9J61_11510, DAH17_03060, DAH23_11200, DAH24_11270, DAH25_12735, DAH26_11215, DAH34_04190, DAH37_16335, DAH42_01565, DAH43_04025, DAH45_06245, DAH46_02630, DAH47_00175, DAH48_03775, DAH49_04030, DAH50_07060, DD762_01090, DEN86_04070, DEN88_16970, DEO18_03405, DKP82_14320, DM870_18070, DN627_10245, DNX30_02270, DTL43_05925, DTL90_09735, DTM45_12630, DU321_03650, DXT70_16925, DXT73_18920, E2112_01240, E2114_18160, E2115_17375, E2116_17400, E2118_15290, E2119_15580, E2120_18200, E2122_04455, E2123_15000, E2124_16685, E2125_17990, E2127_15010, E2128_01350, E2129_02860, E2130_17665, E2131_12060, E2132_15205, E2133_09900, E2134_11975, E2135_11635, E2136_14005, E2646_16160, E3N34_09355, E3O05_11475, E4K51_05790, E4T14_02325, E4T84_08900, E5P22_04090, E5P26_03515, E5P27_14165, E5P28_13975, E5P29_07800, E5P31_13565, E5P32_01560, E5P34_12030, E5P35_01105, E5P36_00515, E5P37_21190, E5P40_07030, E5P52_06840, E5S36_11125, E5S46_19535, E5S51_08280, E5S56_11570, E5S57_07265, E5S58_05605, E5S59_11245, E5S61_20145, E5S62_13855, EA239_13420, EA435_20380, EBP16_09105, ECs0171, ED648_00165, EI021_19845, EIA08_06325, EIZ93_07925, EL79_3705, EL80_3652, ELT16_21255, ELT17_01250, ELT20_04470, ELT21_15045, ELT22_08875, ELT23_12175, ELT24_18805, ELT25_21045, ELT26_05580, ELT27_04470, ELT28_17120, ELT29_02915, ELT30_18440, ELT31_08695, ELT32_04785, ELT33_15870, ELT34_19890, ELT35_06820, ELT36_14035, ELT38_13450, ELT39_20860, ELT40_02130, ELT41_01975, ELT44_21605, ELT45_20715, ELT46_21865, ELT48_12180, ELT49_18475, ELT50_04920, ELT51_07355, ELT52_04135, ELT54_13410, ELT55_19315, ELT56_04940, ELT58_11815, ELT59_17845, ELT60_20950, ELT61_17415, ELT63_15900, ELT72_19820, ELU07_13005, ELU82_16775, ELU83_06360, ELU85_21270, ELU88_20105, ELU89_12520, ELU90_03635, ELU91_18200, ELU94_15810, ELU95_07270, ELU96_20275, ELU97_22275, ELU98_09210, ELU99_07075, ELV00_10925, ELV01_05855, ELV02_21130, ELV03_21785, ELV04_21595, ELV05_06475, ELV07_04595, ELV09_10980, ELV10_05885, ELV11_07295, ELV12_07945, ELV13_13145, ELV15_10275, ELV16_14905, ELV20_03215, ELV21_07905, ELV22_16455, ELV23_20005, ELV26_20305, ELV28_04185, ELV29_15950, ELV40_17635, ELX48_04060, ELX61_13230, ELX66_06730, ELX68_15965, ELX69_11255, ELX76_14550, ELX79_12490, ELX85_10445, ELX96_04945, ELY31_21215, ELY32_08455, ELY36_05095, ELY39_01325, ELY41_06540, ELY48_16915, EPS76_09885, ERS085406_00569, ERS085411_00031, ERS139208_01228, EWK56_14885, ExPECSC038_03990, EXX13_05315, EYV17_16445, EYV18_21745, EYX47_12820, F2N31_00165, F3N40_16020, F7F11_02075, F9B07_03520, F9S83_02275, F9V22_04715, F9V24_09500, F9X20_09355, FA849_08720, FA868_06535, FDM60_08820, FE587_16370, FEJ01_15060, FEL34_01755, FFF58_06185, FGG80_07195, FHD44_14150, FJQ51_00170, FKO60_12340, FOI11_012840, FOI11_22840, FPI65_00925, FQF29_01530, FV293_02895, FY127_02945, FZC17_23565, FZN31_19985, G3565_18165, G3813_000515, G4A38_19340, G5603_21760, GAJ26_21380, GF147_13280, GF199_00160, GF699_14270, GFY34_15725, GGB84_001276, GIB53_10120, GJ11_00885, GKF89_14780, GP711_09530, GQA06_13075, GQM13_12620, GQW07_00970, GQW68_00170, GQW80_13515, GRC73_19590, GRO95_02765, GRW05_07695, GRW57_10410, GSY44_00165, GTP88_05405, GUI33_00165, H0O53_18585, H0O72_10185, H6Y26_004458, HI055_000776, HIE29_003103, HIN64_000550, HIO80_003172, HJ942_003221, HJQ60_000692, HJS37_001627, HJU54_003402, HL563_02735, HL601_07700, HLV18_20625, HLZ50_06960, HmCms169_00360, HMJ82_00170, HMU06_10055, HMV95_04585, HMW38_10575, HNC36_16160, HNC59_20345, HNC66_11685, HNC99_17425, HND12_10355, HV109_19380, HV209_01540, HVV39_17630, HVW04_10225, HVW43_11755, HVX16_21155, HVX31_16115, HVZ30_16745, HVZ71_20400, HX136_20600, I6H00_14085, I6H01_17695, IA00_000033, IFB95_000543, IH768_15385, IH772_14435, IT029_001942, J0541_003915, JNP96_05035, NCTC10082_01383, NCTC10089_04076, NCTC10090_02160, NCTC10767_03962, NCTC10974_04616, NCTC11126_03634, NCTC12950_04424, NCTC13127_05455, NCTC13148_05196, NCTC4450_07399, NCTC7922_05813, NCTC7927_04507, NCTC7928_04613, NCTC8008_03673, NCTC8450_01117, NCTC8500_04546, NCTC8621_04202, NCTC8959_04843, NCTC9037_04189, NCTC9044_03184, NCTC9045_04711, NCTC9117_05053, NCTC9702_04760, NCTC9706_01337, NCTC9775_02328, NCTC9777_00472, SAMEA3472044_04157, SAMEA3472056_00973, SAMEA3472147_00380, SAMEA3751407_04814, SAMEA3752557_00874, SAMEA3753106_03568, TUM18780_36030, WP4S18E07_36950

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Entity ID: 8
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30S ribosomal protein S3H [auth E]233Escherichia coliMutation(s): 0 
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30S ribosomal protein S4I [auth F]206Escherichia coliMutation(s): 0 
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30S ribosomal protein S5J [auth G]167Escherichia coliMutation(s): 0 
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Entity ID: 11
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30S ribosomal protein S6K [auth H]135Escherichia coliMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L2N [auth K]273Escherichia coliMutation(s): 0 
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50S ribosomal protein L3O [auth L]209Escherichia coliMutation(s): 0 
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50S ribosomal protein L4P [auth M]201Escherichia coliMutation(s): 0 
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Entity ID: 17
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50S ribosomal protein L5Q [auth N]179Escherichia coliMutation(s): 0 
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Entity ID: 18
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50S ribosomal protein L6R [auth O]177Escherichia coliMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L9S [auth P]149Escherichia coliMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L31T [auth Q]70Escherichia coliMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L13U [auth R]142Escherichia coliMutation(s): 0 
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Entity ID: 22
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50S ribosomal protein L14V [auth S]123Escherichia coliMutation(s): 0 
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Entity ID: 23
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50S ribosomal protein L15W [auth T]144Escherichia coliMutation(s): 0 
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Entity ID: 24
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50S ribosomal protein L16X [auth U]136Escherichia coliMutation(s): 0 
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Entity ID: 25
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50S ribosomal protein L17Y [auth V]127Escherichia coliMutation(s): 0 
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Entity ID: 26
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50S ribosomal protein L18Z [auth W]117Escherichia coliMutation(s): 0 
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Entity ID: 27
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50S ribosomal protein L19AA [auth X]115Escherichia coliMutation(s): 0 
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Entity ID: 28
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50S ribosomal protein L20BA [auth Y]118Escherichia coliMutation(s): 0 
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Entity ID: 29
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Ribosomal protein L21CA [auth Z]103Escherichia coliMutation(s): 0 
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Entity ID: 30
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50S ribosomal protein L22DA [auth a]110Escherichia coliMutation(s): 0 
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Entity ID: 31
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50S ribosomal protein L23EA [auth b]100Escherichia coliMutation(s): 0 
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Entity ID: 32
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50S ribosomal protein L24FA [auth c]104Escherichia coliMutation(s): 0 
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Entity ID: 33
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50S ribosomal protein L25GA [auth d]94Escherichia coliMutation(s): 0 
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Entity ID: 34
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50S ribosomal protein L27HA [auth e]85Escherichia coliMutation(s): 0 
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Entity ID: 35
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50S ribosomal protein L28IA [auth f]78Escherichia coliMutation(s): 0 
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Entity ID: 36
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50S ribosomal protein L29JA [auth g]63Escherichia coliMutation(s): 0 
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Entity ID: 37
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50S ribosomal protein L30KA [auth h]59Escherichia coliMutation(s): 0 
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Entity ID: 38
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50S ribosomal protein L32LA [auth i]57Escherichia coliMutation(s): 0 
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UniProt GroupD7XI28
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Entity ID: 39
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50S ribosomal protein L33MA [auth j]55Escherichia coliMutation(s): 0 
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Entity ID: 40
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50S ribosomal protein L34NA [auth k]46Escherichia coliMutation(s): 0 
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Entity ID: 41
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50S ribosomal protein L35OA [auth l]65Escherichia coliMutation(s): 0 
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Entity ID: 42
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50S ribosomal protein L36PA [auth m]38Escherichia coliMutation(s): 0 
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Entity ID: 43
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30S ribosomal protein S7QA [auth n]179Escherichia coliMutation(s): 0 
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Entity ID: 44
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30S ribosomal protein S8RA [auth o]130Escherichia coliMutation(s): 0 
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Entity ID: 45
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30S ribosomal protein S9SA [auth p]130Escherichia coliMutation(s): 0 
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Entity ID: 46
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30S ribosomal protein S10TA [auth q]103Escherichia coliMutation(s): 0 
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Entity ID: 47
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30S ribosomal protein S11UA [auth r]129Escherichia coliMutation(s): 0 
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Entity ID: 48
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nascent peptide chainVA [auth s]5Escherichia coliMutation(s): 0 
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Entity ID: 49
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30S ribosomal protein S12WA [auth t]124Escherichia coliMutation(s): 0 
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Entity ID: 50
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30S ribosomal protein S13XA [auth u]118Escherichia coliMutation(s): 0 
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Entity ID: 51
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30S ribosomal protein S14YA [auth v]101Escherichia coliMutation(s): 0 
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Entity ID: 52
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30S ribosomal protein S15ZA [auth w]89Escherichia coliMutation(s): 0 
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Entity ID: 53
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30S ribosomal protein S16AB [auth x]82Escherichia coliMutation(s): 0 
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Entity ID: 54
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30S ribosomal protein S17BB [auth y]84Escherichia coliMutation(s): 0 
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Entity ID: 55
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30S ribosomal protein S18CB [auth z]75Escherichia coliMutation(s): 0 
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Entity ID: 4
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mRNAD [auth 4]15Escherichia coli
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Entity ID: 5
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tRNA(PHE)E [auth A]76Escherichia coli
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Entity ID: 6
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16S rRNAF [auth C]1,540Escherichia coli
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Entity ID: 12
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23S rRNAL [auth I]2,904Escherichia coli
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Entity ID: 13
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5S rRNAM [auth J]120Escherichia coli
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RD8 (Subject of Investigation/LOI)
Query on RD8
Download Ideal Coordinates CCD File 
BJ [auth I]Radezolid
C22 H23 F N6 O3
BTTNOGHPGJANSW-IBGZPJMESA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EJ [auth Q],
GJ [auth m]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AC [auth C],
AD [auth C],
AE [auth C],
AF [auth I],
AG [auth I],
AC [auth C],
AD [auth C],
AE [auth C],
AF [auth I],
AG [auth I],
AH [auth I],
AI [auth I],
AJ [auth I],
BC [auth C],
BD [auth C],
BE [auth C],
BF [auth I],
BG [auth I],
BH [auth I],
BI [auth I],
CC [auth C],
CD [auth C],
CE [auth C],
CF [auth I],
CG [auth I],
CH [auth I],
CI [auth I],
CJ [auth K],
DB [auth C],
DC [auth C],
DD [auth C],
DE [auth C],
DF [auth I],
DG [auth I],
DH [auth I],
DI [auth I],
DJ [auth L],
EB [auth C],
EC [auth C],
ED [auth C],
EE [auth C],
EF [auth I],
EG [auth I],
EH [auth I],
EI [auth I],
FB [auth C],
FC [auth C],
FD [auth C],
FE [auth C],
FF [auth I],
FG [auth I],
FH [auth I],
FI [auth I],
FJ [auth V],
GB [auth C],
GC [auth C],
GD [auth C],
GE [auth C],
GF [auth I],
GG [auth I],
GH [auth I],
GI [auth I],
HB [auth C],
HC [auth C],
HD [auth C],
HE [auth C],
HF [auth I],
HG [auth I],
HH [auth I],
HI [auth I],
IB [auth C],
IC [auth C],
ID [auth C],
IE [auth C],
IF [auth I],
IG [auth I],
IH [auth I],
II [auth I],
JB [auth C],
JC [auth C],
JD [auth C],
JE [auth C],
JF [auth I],
JG [auth I],
JH [auth I],
JI [auth I],
KB [auth C],
KC [auth C],
KD [auth C],
KE [auth C],
KF [auth I],
KG [auth I],
KH [auth I],
KI [auth I],
LB [auth C],
LC [auth C],
LD [auth C],
LE [auth C],
LF [auth I],
LG [auth I],
LH [auth I],
LI [auth I],
MB [auth C],
MC [auth C],
MD [auth C],
ME [auth C],
MF [auth I],
MG [auth I],
MH [auth I],
MI [auth I],
NB [auth C],
NC [auth C],
ND [auth C],
NE [auth C],
NF [auth I],
NG [auth I],
NH [auth I],
NI [auth I],
OB [auth C],
OC [auth C],
OD [auth C],
OE [auth C],
OF [auth I],
OG [auth I],
OH [auth I],
OI [auth I],
PB [auth C],
PC [auth C],
PD [auth C],
PE [auth C],
PF [auth I],
PG [auth I],
PH [auth I],
PI [auth I],
QB [auth C],
QC [auth C],
QD [auth C],
QE [auth C],
QF [auth I],
QG [auth I],
QH [auth I],
QI [auth I],
RB [auth C],
RC [auth C],
RD [auth C],
RE [auth C],
RF [auth I],
RG [auth I],
RH [auth I],
RI [auth I],
SB [auth C],
SC [auth C],
SD [auth C],
SE [auth I],
SF [auth I],
SG [auth I],
SH [auth I],
SI [auth I],
TB [auth C],
TC [auth C],
TD [auth C],
TE [auth I],
TF [auth I],
TG [auth I],
TH [auth I],
TI [auth I],
UB [auth C],
UC [auth C],
UD [auth C],
UE [auth I],
UF [auth I],
UG [auth I],
UH [auth I],
UI [auth I],
VB [auth C],
VC [auth C],
VD [auth C],
VE [auth I],
VF [auth I],
VG [auth I],
VH [auth I],
VI [auth I],
WB [auth C],
WC [auth C],
WD [auth C],
WE [auth I],
WF [auth I],
WG [auth I],
WH [auth I],
WI [auth I],
XB [auth C],
XC [auth C],
XD [auth C],
XE [auth I],
XF [auth I],
XG [auth I],
XH [auth I],
XI [auth I],
YB [auth C],
YC [auth C],
YD [auth C],
YE [auth I],
YF [auth I],
YG [auth I],
YH [auth I],
YI [auth I],
ZB [auth C],
ZC [auth C],
ZD [auth C],
ZE [auth I],
ZF [auth I],
ZG [auth I],
ZH [auth I],
ZI [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
4D4
Query on 4D4		X [auth U]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.48 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2
MODEL REFINEMENTISOLDE1.2.2
RECONSTRUCTIONcisTEMv1.0.0-beta

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI137270
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F32AI148120
Other governmentS10OD020054
Other governmentS10OD021741
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129539
Simons FoundationSF349247
W. M. Keck FoundationMedical Research Grant
Other privateSangvhi-Agarwal Innovation Award
National Science Foundation (NSF, United States)GRFP
Other privateUCSF Discovery Fellowship

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references