4V7S

Crystal structure of the E. coli ribosome bound to telithromycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 

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Literature

Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.

Dunkle, J.A.Xiong, L.Mankin, A.S.Cate, J.H.

(2010) Proc Natl Acad Sci U S A 107: 17152-17157

  • DOI: 10.1073/pnas.1007988107
  • Primary Citation of Related Structures:  
    4V7S, 4V7T, 4V7U, 4V7V

  • PubMed Abstract: 
  • Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets ...

    Differences between the structures of bacterial, archaeal, and eukaryotic ribosomes account for the selective action of antibiotics. Even minor variations in the structure of ribosomes of different bacterial species may lead to idiosyncratic, species-specific interactions of the drugs with their targets. Although crystallographic structures of antibiotics bound to the peptidyl transferase center or the exit tunnel of archaeal (Haloarcula marismortui) and bacterial (Deinococcus radiodurans) large ribosomal subunits have been reported, it remains unclear whether the interactions of antibiotics with these ribosomes accurately reflect those with the ribosomes of pathogenic bacteria. Here we report X-ray crystal structures of the Escherichia coli ribosome in complexes with clinically important antibiotics of four major classes, including the macrolide erythromycin, the ketolide telithromycin, the lincosamide clindamycin, and a phenicol, chloramphenicol, at resolutions of ∼3.3 Å-3.4 Å. Binding modes of three of these antibiotics show important variations compared to the previously determined structures. Biochemical and structural evidence also indicates that interactions of telithromycin with the E. coli ribosome more closely resembles drug binding to ribosomes of bacterial pathogens. The present data further argue that the identity of nucleotides 752, 2609, and 2055 of 23S ribosomal RNA explain in part the spectrum and selectivity of antibiotic action.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.



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Entity ID: 2
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30S ribosomal protein S2B [auth AB], BB [auth CB]218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3C [auth AC], CB [auth CC]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4D [auth AD], DB [auth CD]205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5E [auth AE], EB [auth CE]150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6F [auth AF], FB [auth CF]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7G [auth AG]151Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8H [auth AH], HB [auth CH]129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9I [auth AI], IB [auth CI]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10J [auth AJ], JB [auth CJ]98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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30S ribosomal protein S11K [auth AK], KB [auth CK]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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30S ribosomal protein S12L [auth AL], LB [auth CL]123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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30S ribosomal protein S13M [auth AM]114Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S14N [auth AN], NB [auth CN]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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30S ribosomal protein S15O [auth AO], OB [auth CO]88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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30S ribosomal protein S16P [auth AP]82Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17Q [auth AQ], QB [auth CQ]80Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S18R [auth AR], RB [auth CR]55Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S19S [auth AS], SB [auth CS]79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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30S ribosomal protein S20T [auth AT], TB [auth CT]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21U [auth AU], UB [auth CU]51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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50S ribosomal protein L2X [auth BC], XB [auth DC]271Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3Y [auth BD], YB [auth DD]209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4Z [auth BE], ZB [auth DE]201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5AA [auth BF]177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6BA [auth BG], BC [auth DG]176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9CA [auth BH], CC [auth DH]149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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50S ribosomal protein L11DA [auth BI], DC [auth DI]141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13EA [auth BJ], EC [auth DJ]142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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50S ribosomal protein L14FA [auth BK], FC [auth DK]122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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50S ribosomal protein L15GA [auth BL], GC [auth DL]143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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50S ribosomal protein L16HA [auth BM], HC [auth DM]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17IA [auth BN], IC [auth DN]120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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50S ribosomal protein L18JA [auth BO], JC [auth DO]116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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50S ribosomal protein L19KA [auth BP], KC [auth DP]114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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50S ribosomal protein L20LA [auth BQ], LC [auth DQ]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21MA [auth BR], MC [auth DR]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22NA [auth BS], NC [auth DS]110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23OA [auth BT], OC [auth DT]93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24PA [auth BU], PC [auth DU]102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25QA [auth BV], QC [auth DV]94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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50S ribosomal protein L27RA [auth BW], RC [auth DW]79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28SA [auth BX], SC [auth DX]77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29TA [auth BY], TC [auth DY]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30UA [auth BZ], UC [auth DZ]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32VA [auth B0], VC [auth D0]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33WA [auth B1], WC [auth D1]50Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34XA [auth B2], XC [auth D2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35YA [auth B3], YC [auth D3]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36ZA [auth B4], ZC [auth D4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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30S ribosomal protein S7GB [auth CG]150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 55
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30S ribosomal protein S13MB [auth CM]113Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Find proteins for P0A7S9 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16PB [auth CP]80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Find proteins for P0A7T3 (Escherichia coli (strain K12))
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5AC [auth DF]178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
UniProt
Find proteins for P62399 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth AA]1533Escherichia coli
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Entity ID: 22
MoleculeChainsLengthOrganismImage
23S rRNAV [auth BA], VB [auth DA]2903Escherichia coli
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Entity ID: 23
MoleculeChainsLengthOrganismImage
5S rRNAW [auth BB]118Escherichia coli K-12
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Entity ID: 53
MoleculeChainsLengthOrganismImage
16S rRNAAB [auth CA]1530Escherichia coli
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Entity ID: 57
MoleculeChainsLengthOrganismImage
5S rRNAWB [auth DB]117Escherichia coli K-12
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEL (Subject of Investigation/LOI)
Query on TEL

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VJ [auth BA]TELITHROMYCIN
C43 H65 N5 O10
LJVAJPDWBABPEJ-PNUFFHFMSA-N
 Ligand Interaction
ZN
Query on ZN

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AK [auth B4], YQ [auth D4]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth AA] , AE [auth AA] , AF [auth BA] , AG [auth BA] , AH [auth BA] , AI [auth BA] , AJ [auth BA] , AL [auth CA] , 
AD [auth AA], AE [auth AA], AF [auth BA], AG [auth BA], AH [auth BA], AI [auth BA], AJ [auth BA], AL [auth CA], AM [auth DA], AN [auth DA], AO [auth DA], AP [auth DA], AQ [auth DA], BD [auth AA], BE [auth AA], BF [auth BA], BG [auth BA], BH [auth BA], BI [auth BA], BJ [auth BA], BK [auth CA], BL [auth CA], BM [auth DA], BN [auth DA], BO [auth DA], BP [auth DA], BQ [auth DA], CD [auth AA], CE [auth AA], CF [auth BA], CG [auth BA], CH [auth BA], CI [auth BA], CJ [auth BA], CK [auth CA], CL [auth CA], CM [auth DA], CN [auth DA], CO [auth DA], CP [auth DA], CQ [auth DA], DD [auth AA], DE [auth AA], DF [auth BA], DG [auth BA], DH [auth BA], DI [auth BA], DJ [auth BA], DK [auth CA], DL [auth CA], DM [auth DA], DN [auth DA], DO [auth DA], DP [auth DA], DQ [auth DA], ED [auth AA], EE [auth AA], EF [auth BA], EG [auth BA], EH [auth BA], EI [auth BA], EJ [auth BA], EK [auth CA], EL [auth CA], EM [auth DA], EN [auth DA], EO [auth DA], EP [auth DA], EQ [auth DA], FD [auth AA], FE [auth AA], FF [auth BA], FG [auth BA], FH [auth BA], FI [auth BA], FJ [auth BA], FK [auth CA], FL [auth CA], FM [auth DA], FN [auth DA], FO [auth DA], FP [auth DA], FQ [auth DA], GD [auth AA], GE [auth AA], GF [auth BA], GG [auth BA], GH [auth BA], GI [auth BA], GJ [auth BA], GK [auth CA], GL [auth CA], GM [auth DA], GN [auth DA], GO [auth DA], GP [auth DA], GQ [auth DA], HD [auth AA], HE [auth AA], HF [auth BA], HG [auth BA], HH [auth BA], HI [auth BA], HJ [auth BA], HK [auth CA], HL [auth CA], HM [auth DA], HN [auth DA], HO [auth DA], HP [auth DA], HQ [auth DA], ID [auth AA], IE [auth AA], IF [auth BA], IG [auth BA], IH [auth BA], II [auth BA], IJ [auth BA], IK [auth CA], IL [auth CA], IM [auth DA], IN [auth DA], IO [auth DA], IP [auth DA], IQ [auth DA], JD [auth AA], JE [auth AA], JF [auth BA], JG [auth BA], JH [auth BA], JI [auth BA], JJ [auth BA], JK [auth CA], JL [auth CA], JM [auth DA], JN [auth DA], JO [auth DA], JP [auth DA], JQ [auth DA], KD [auth AA], KE [auth AA], KF [auth BA], KG [auth BA], KH [auth BA], KI [auth BA], KJ [auth BA], KK [auth CA], KL [auth CA], KM [auth DA], KN [auth DA], KO [auth DA], KP [auth DA], KQ [auth DA], LD [auth AA], LE [auth AA], LF [auth BA], LG [auth BA], LH [auth BA], LI [auth BA], LJ [auth BA], LK [auth CA], LL [auth CA], LM [auth DA], LN [auth DA], LO [auth DA], LP [auth DA], LQ [auth DA], MD [auth AA], ME [auth AA], MF [auth BA], MG [auth BA], MH [auth BA], MI [auth BA], MJ [auth BA], MK [auth CA], ML [auth CA], MM [auth DA], MN [auth DA], MO [auth DA], MP [auth DA], MQ [auth DA], ND [auth AA], NE [auth AA], NF [auth BA], NG [auth BA], NH [auth BA], NI [auth BA], NJ [auth BA], NK [auth CA], NL [auth CA], NM [auth DA], NN [auth DA], NO [auth DA], NP [auth DA], NQ [auth DA], OD [auth AA], OE [auth AA], OF [auth BA], OG [auth BA], OH [auth BA], OI [auth BA], OJ [auth BA], OK [auth CA], OL [auth CA], OM [auth DA], ON [auth DA], OO [auth DA], OP [auth DA], OQ [auth DA], PD [auth AA], PE [auth AA], PF [auth BA], PG [auth BA], PH [auth BA], PI [auth BA], PJ [auth BA], PK [auth CA], PL [auth CA], PM [auth DA], PN [auth DA], PO [auth DA], PP [auth DA], PQ [auth DA], QD [auth AA], QE [auth AA], QF [auth BA], QG [auth BA], QH [auth BA], QI [auth BA], QJ [auth BA], QK [auth CA], QL [auth CE], QM [auth DA], QN [auth DA], QO [auth DA], QP [auth DA], QQ [auth DA], RD [auth AA], RE [auth BA], RF [auth BA], RG [auth BA], RH [auth BA], RI [auth BA], RJ [auth BA], RK [auth CA], RL [auth DA], RM [auth DA], RN [auth DA], RO [auth DA], RP [auth DA], RQ [auth DA], SD [auth AA], SE [auth BA], SF [auth BA], SG [auth BA], SH [auth BA], SI [auth BA], SJ [auth BA], SK [auth CA], SL [auth DA], SM [auth DA], SN [auth DA], SO [auth DA], SP [auth DA], SQ [auth DA], TD [auth AA], TE [auth BA], TF [auth BA], TG [auth BA], TH [auth BA], TI [auth BA], TJ [auth BA], TK [auth CA], TL [auth DA], TM [auth DA], TN [auth DA], TO [auth DA], TP [auth DA], TQ [auth DA], UD [auth AA], UE [auth BA], UF [auth BA], UG [auth BA], UH [auth BA], UI [auth BA], UJ [auth BA], UK [auth CA], UL [auth DA], UM [auth DA], UN [auth DA], UO [auth DA], UP [auth DA], UQ [auth DB], VD [auth AA], VE [auth BA], VF [auth BA], VG [auth BA], VH [auth BA], VI [auth BA], VK [auth CA], VL [auth DA], VM [auth DA], VN [auth DA], VO [auth DA], VP [auth DA], VQ [auth DC], WD [auth AA], WE [auth BA], WF [auth BA], WG [auth BA], WH [auth BA], WI [auth BA], WJ [auth BB], WK [auth CA], WL [auth DA], WM [auth DA], WN [auth DA], WO [auth DA], WP [auth DA], WQ [auth DC], XD [auth AA], XE [auth BA], XF [auth BA], XG [auth BA], XH [auth BA], XI [auth BA], XJ [auth BB], XK [auth CA], XL [auth DA], XM [auth DA], XN [auth DA], XO [auth DA], XP [auth DA], XQ [auth DJ], YD [auth AA], YE [auth BA], YF [auth BA], YG [auth BA], YH [auth BA], YI [auth BA], YJ [auth BB], YK [auth CA], YL [auth DA], YM [auth DA], YN [auth DA], YO [auth DA], YP [auth DA], ZD [auth AA], ZE [auth BA], ZF [auth BA], ZG [auth BA], ZH [auth BA], ZI [auth BA], ZJ [auth BB], ZK [auth CA], ZL [auth DA], ZM [auth DA], ZN [auth DA], ZO [auth DA], ZP [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.759α = 90
b = 433.272β = 90
c = 618.863γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2021-01-27
    Changes: Data collection, Derived calculations, Structure summary