4U26

Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Synergy of streptogramin antibiotics occurs independently of their effects on translation.

Noeske, J.Huang, J.Olivier, N.B.Giacobbe, R.A.Zambrowski, M.Cate, J.H.

(2014) Antimicrob Agents Chemother 58: 5269-5279

  • DOI: 10.1128/AAC.03389-14
  • Primary Citation of Related Structures:  
    4U1U, 4U1V, 4U20, 4U24, 4U25, 4U26, 4U27

  • PubMed Abstract: 
  • Streptogramin antibiotics are divided into types A and B, which in combination can act synergistically. We compared the molecular interactions of the streptogramin combinations Synercid (type A, dalfopristin; type B, quinupristin) and NXL 103 (type A, flopristin; type B, linopristin) with the Escherichia coli 70S ribosome by X-ray crystallography ...

    Streptogramin antibiotics are divided into types A and B, which in combination can act synergistically. We compared the molecular interactions of the streptogramin combinations Synercid (type A, dalfopristin; type B, quinupristin) and NXL 103 (type A, flopristin; type B, linopristin) with the Escherichia coli 70S ribosome by X-ray crystallography. We further analyzed the activity of the streptogramin components individually and in combination. The streptogramin A and B components in Synercid and NXL 103 exhibit synergistic antimicrobial activity against certain pathogenic bacteria. However, in transcription-coupled translation assays, only combinations that include dalfopristin, the streptogramin A component of Synercid, show synergy. Notably, the diethylaminoethylsulfonyl group in dalfopristin reduces its activity but is the basis for synergy in transcription-coupled translation assays before its rapid hydrolysis from the depsipeptide core. Replacement of the diethylaminoethylsulfonyl group in dalfopristin by a nonhydrolyzable group may therefore be beneficial for synergy. The absence of general streptogramin synergy in transcription-coupled translation assays suggests that the synergistic antimicrobial activity of streptogramins can occur independently of the effects of streptogramin on translation.


    Organizational Affiliation

    Department of Molecular Cell Biology, California Institute of Quantitative Biosciences, University of California, Berkeley, California, USA jcate@lbl.gov.



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30S ribosomal protein S2B [auth AB], DB [auth CB]218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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30S ribosomal protein S3C [auth AC], EB [auth CC]206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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30S ribosomal protein S4D [auth AD], FB [auth CD]205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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30S ribosomal protein S5E [auth AE], GB [auth CE]150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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30S ribosomal protein S6F [auth AF], HB [auth CF]100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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30S ribosomal protein S7G [auth AG], IB [auth CG]151Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S8H [auth AH], JB [auth CH]129Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S9I [auth AI], KB [auth CI]127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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30S ribosomal protein S10J [auth AJ], LB [auth CJ]98Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S11K [auth AK], MB [auth CK]117Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S12L [auth AL], NB [auth CL]123Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S13M [auth AM], OB [auth CM]114Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S14N [auth AN], PB [auth CN]100Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S15O [auth AO], QB [auth CO]88Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S16P [auth AP], RB [auth CP]82Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S17Q [auth AQ], SB [auth CQ]80Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S18R [auth AR], TB [auth CR]55Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S19S [auth AS], UB [auth CS]79Escherichia coli K-12Mutation(s): 0 
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30S ribosomal protein S20T [auth AT], VB [auth CT]85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21U [auth AU], WB [auth CU]51Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L2X [auth BC], ZB [auth DC]271Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L3Y [auth BD], AC [auth DD]209Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L4Z [auth BE], BC [auth DE]201Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L5AA [auth BF], CC [auth DF]177Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L6BA [auth BG], DC [auth DG]176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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50S ribosomal protein L9CA [auth BH], EC [auth DH]149Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L11DA [auth BI], FC [auth DI]141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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50S ribosomal protein L13EA [auth BJ], GC [auth DJ]142Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L14FA [auth BK], HC [auth DK]122Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L15GA [auth BL], IC [auth DL]143Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L16HA [auth BM], JC [auth DM]136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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50S ribosomal protein L17IA [auth BN], KC [auth DN]120Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L18JA [auth BO], LC [auth DO]116Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L19KA [auth BP], MC [auth DP]114Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L20LA [auth BQ], NC [auth DQ]117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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50S ribosomal protein L21MA [auth BR], OC [auth DR]103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22NA [auth BS], PC [auth DS]110Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L23OA [auth BT], QC [auth DT]93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24PA [auth BU], RC [auth DU]102Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L25QA [auth BV], SC [auth DV]94Escherichia coli K-12Mutation(s): 0 
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50S ribosomal protein L27RA [auth BW], TC [auth DW]76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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50S ribosomal protein L28SA [auth BX], UC [auth DX]77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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50S ribosomal protein L29TA [auth BY], VC [auth DY]63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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50S ribosomal protein L30UA [auth BZ], WC [auth DZ]58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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50S ribosomal protein L32VA [auth B0], XC [auth D0]56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33WA [auth B1], YC [auth D1]50Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34XA [auth B2], ZC [auth D2]46Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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50S ribosomal protein L35YA [auth B3], AD [auth D3]64Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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50S ribosomal protein L36ZA [auth B4], BD [auth D4]38Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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50S ribosomal protein L1AB [auth B5]228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
UniProt
Find proteins for Q5SLP7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLP7 
Go to UniProtKB:  Q5SLP7
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  • Reference Sequence

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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
QuinupristinBB [auth B6], CD [auth D6]8synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAA [auth AA], CB [auth CA]1539Escherichia coli str. K-12 substr. MDS42
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Entity ID: 22
MoleculeChainsLengthOrganismImage
23S rRNAV [auth BA], XB [auth DA]2903Escherichia coli str. K-12 substr. MDS42
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Entity ID: 23
MoleculeChainsLengthOrganismImage
5S rRNAW [auth BB], YB [auth DB]119Escherichia coli str. K-12 substr. MDS42
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOL (Subject of Investigation/LOI)
Query on DOL

Download Ideal Coordinates CCD File 
UP [auth DA], XF [auth BA]5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE
C34 H50 N4 O9 S
SUYRLXYYZQTJHF-VMBLUXKRSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
KW [auth D4], PN [auth B4]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AE [auth AA] , AF [auth AA] , AG [auth BA] , AH [auth BA] , AI [auth BA] , AJ [auth BA] , AK [auth BA] , AL [auth BA] , 
AE [auth AA], AF [auth AA], AG [auth BA], AH [auth BA], AI [auth BA], AJ [auth BA], AK [auth BA], AL [auth BA], AM [auth BA], AN [auth BA], AO [auth CA], AP [auth CA], AQ [auth DA], AR [auth DA], AS [auth DA], AT [auth DA], AU [auth DA], AV [auth DA], AW [auth DA], BE [auth AA], BF [auth AA], BG [auth BA], BH [auth BA], BI [auth BA], BJ [auth BA], BK [auth BA], BL [auth BA], BM [auth BA], BN [auth BA], BO [auth CA], BP [auth CA], BQ [auth DA], BR [auth DA], BS [auth DA], BT [auth DA], BU [auth DA], BV [auth DA], BW [auth DA], CE [auth AA], CF [auth AA], CG [auth BA], CH [auth BA], CI [auth BA], CJ [auth BA], CK [auth BA], CL [auth BA], CM [auth BA], CN [auth BA], CO [auth CA], CP [auth CA], CQ [auth DA], CR [auth DA], CS [auth DA], CT [auth DA], CU [auth DA], CV [auth DA], CW [auth DA], DD [auth AA], DE [auth AA], DF [auth AA], DG [auth BA], DH [auth BA], DI [auth BA], DJ [auth BA], DK [auth BA], DL [auth BA], DM [auth BA], DN [auth BA], DO [auth CA], DP [auth CA], DQ [auth DA], DR [auth DA], DS [auth DA], DT [auth DA], DU [auth DA], DV [auth DA], DW [auth DA], ED [auth AA], EE [auth AA], EF [auth AA], EG [auth BA], EH [auth BA], EI [auth BA], EJ [auth BA], EK [auth BA], EL [auth BA], EM [auth BA], EN [auth BA], EO [auth CA], EP [auth CA], EQ [auth DA], ER [auth DA], ES [auth DA], ET [auth DA], EU [auth DA], EV [auth DA], EW [auth DA], FD [auth AA], FE [auth AA], FF [auth AA], FG [auth BA], FH [auth BA], FI [auth BA], FJ [auth BA], FK [auth BA], FL [auth BA], FM [auth BA], FN [auth BA], FO [auth CA], FP [auth CA], FQ [auth DA], FR [auth DA], FS [auth DA], FT [auth DA], FU [auth DA], FV [auth DA], FW [auth DB], GD [auth AA], GE [auth AA], GF [auth AA], GG [auth BA], GH [auth BA], GI [auth BA], GJ [auth BA], GK [auth BA], GL [auth BA], GM [auth BA], GN [auth BA], GO [auth CA], GP [auth CA], GQ [auth DA], GR [auth DA], GS [auth DA], GT [auth DA], GU [auth DA], GV [auth DA], GW [auth DB], HD [auth AA], HE [auth AA], HF [auth AA], HG [auth BA], HH [auth BA], HI [auth BA], HJ [auth BA], HK [auth BA], HL [auth BA], HM [auth BA], HN [auth BA], HO [auth CA], HP [auth CA], HQ [auth DA], HR [auth DA], HS [auth DA], HT [auth DA], HU [auth DA], HV [auth DA], HW [auth DB], ID [auth AA], IE [auth AA], IF [auth AA], IG [auth BA], IH [auth BA], II [auth BA], IJ [auth BA], IK [auth BA], IL [auth BA], IM [auth BA], IN [auth BA], IO [auth CA], IP [auth CA], IQ [auth DA], IR [auth DA], IS [auth DA], IT [auth DA], IU [auth DA], IV [auth DA], IW [auth DQ], JD [auth AA], JE [auth AA], JF [auth AA], JG [auth BA], JH [auth BA], JI [auth BA], JJ [auth BA], JK [auth BA], JL [auth BA], JM [auth BA], JN [auth BA], JO [auth CA], JP [auth CA], JQ [auth DA], JR [auth DA], JS [auth DA], JT [auth DA], JU [auth DA], JV [auth DA], JW [auth D2], KD [auth AA], KE [auth AA], KF [auth AA], KG [auth BA], KH [auth BA], KI [auth BA], KJ [auth BA], KK [auth BA], KL [auth BA], KM [auth BA], KN [auth BB], KO [auth CA], KP [auth CA], KQ [auth DA], KR [auth DA], KS [auth DA], KT [auth DA], KU [auth DA], KV [auth DA], LD [auth AA], LE [auth AA], LF [auth AA], LG [auth BA], LH [auth BA], LI [auth BA], LJ [auth BA], LK [auth BA], LL [auth BA], LM [auth BA], LN [auth BB], LO [auth CA], LP [auth CA], LQ [auth DA], LR [auth DA], LS [auth DA], LT [auth DA], LU [auth DA], LV [auth DA], MD [auth AA], ME [auth AA], MF [auth AA], MG [auth BA], MH [auth BA], MI [auth BA], MJ [auth BA], MK [auth BA], ML [auth BA], MM [auth BA], MN [auth BB], MO [auth CA], MP [auth CA], MQ [auth DA], MR [auth DA], MS [auth DA], MT [auth DA], MU [auth DA], MV [auth DA], ND [auth AA], NE [auth AA], NF [auth AA], NG [auth BA], NH [auth BA], NI [auth BA], NJ [auth BA], NK [auth BA], NL [auth BA], NM [auth BA], NN [auth BB], NO [auth CA], NP [auth CA], NQ [auth DA], NR [auth DA], NS [auth DA], NT [auth DA], NU [auth DA], NV [auth DA], OD [auth AA], OE [auth AA], OF [auth AA], OG [auth BA], OH [auth BA], OI [auth BA], OJ [auth BA], OK [auth BA], OL [auth BA], OM [auth BA], ON [auth BQ], OO [auth CA], OP [auth CA], OQ [auth DA], OR [auth DA], OS [auth DA], OT [auth DA], OU [auth DA], OV [auth DA], PD [auth AA], PE [auth AA], PF [auth AA], PG [auth BA], PH [auth BA], PI [auth BA], PJ [auth BA], PK [auth BA], PL [auth BA], PM [auth BA], PO [auth CA], PP [auth CA], PQ [auth DA], PR [auth DA], PS [auth DA], PT [auth DA], PU [auth DA], PV [auth DA], QD [auth AA], QE [auth AA], QF [auth AA], QG [auth BA], QH [auth BA], QI [auth BA], QJ [auth BA], QK [auth BA], QL [auth BA], QM [auth BA], QN [auth CA], QO [auth CA], QP [auth CA], QQ [auth DA], QR [auth DA], QS [auth DA], QT [auth DA], QU [auth DA], QV [auth DA], RD [auth AA], RE [auth AA], RF [auth AA], RG [auth BA], RH [auth BA], RI [auth BA], RJ [auth BA], RK [auth BA], RL [auth BA], RM [auth BA], RN [auth CA], RO [auth CA], RP [auth CA], RQ [auth DA], RR [auth DA], RS [auth DA], RT [auth DA], RU [auth DA], RV [auth DA], SD [auth AA], SE [auth AA], SF [auth AA], SG [auth BA], SH [auth BA], SI [auth BA], SJ [auth BA], SK [auth BA], SL [auth BA], SM [auth BA], SN [auth CA], SO [auth CA], SP [auth CA], SQ [auth DA], SR [auth DA], SS [auth DA], ST [auth DA], SU [auth DA], SV [auth DA], TD [auth AA], TE [auth AA], TF [auth AA], TG [auth BA], TH [auth BA], TI [auth BA], TJ [auth BA], TK [auth BA], TL [auth BA], TM [auth BA], TN [auth CA], TO [auth CA], TP [auth CA], TQ [auth DA], TR [auth DA], TS [auth DA], TT [auth DA], TU [auth DA], TV [auth DA], UD [auth AA], UE [auth AA], UF [auth AA], UG [auth BA], UH [auth BA], UI [auth BA], UJ [auth BA], UK [auth BA], UL [auth BA], UM [auth BA], UN [auth CA], UO [auth CA], UQ [auth DA], UR [auth DA], US [auth DA], UT [auth DA], UU [auth DA], UV [auth DA], VD [auth AA], VE [auth AA], VF [auth AA], VG [auth BA], VH [auth BA], VI [auth BA], VJ [auth BA], VK [auth BA], VL [auth BA], VM [auth BA], VN [auth CA], VO [auth CA], VP [auth DA], VQ [auth DA], VR [auth DA], VS [auth DA], VT [auth DA], VU [auth DA], VV [auth DA], WD [auth AA], WE [auth AA], WF [auth AM], WG [auth BA], WH [auth BA], WI [auth BA], WJ [auth BA], WK [auth BA], WL [auth BA], WM [auth BA], WN [auth CA], WO [auth CA], WP [auth DA], WQ [auth DA], WR [auth DA], WS [auth DA], WT [auth DA], WU [auth DA], WV [auth DA], XD [auth AA], XE [auth AA], XG [auth BA], XH [auth BA], XI [auth BA], XJ [auth BA], XK [auth BA], XL [auth BA], XM [auth BA], XN [auth CA], XO [auth CA], XP [auth DA], XQ [auth DA], XR [auth DA], XS [auth DA], XT [auth DA], XU [auth DA], XV [auth DA], YD [auth AA], YE [auth AA], YF [auth BA], YG [auth BA], YH [auth BA], YI [auth BA], YJ [auth BA], YK [auth BA], YL [auth BA], YM [auth BA], YN [auth CA], YO [auth CA], YP [auth DA], YQ [auth DA], YR [auth DA], YS [auth DA], YT [auth DA], YU [auth DA], YV [auth DA], ZD [auth AA], ZE [auth AA], ZF [auth BA], ZG [auth BA], ZH [auth BA], ZI [auth BA], ZJ [auth BA], ZK [auth BA], ZL [auth BA], ZM [auth BA], ZN [auth CA], ZO [auth CA], ZP [auth DA], ZQ [auth DA], ZR [auth DA], ZS [auth DA], ZT [auth DA], ZU [auth DA], ZV [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MHU
Query on MHU
BB [auth B6], CD [auth D6]L-PEPTIDE LINKINGC12 H18 N2 O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 54
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000505
Query on PRD_000505
BB [auth B6], CD [auth D6]QuinupristinOligopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.26α = 90
b = 432.34β = 90
c = 621.39γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2014-12-10
    Changes: Other
  • Version 1.3: 2015-04-22
    Changes: Structure summary
  • Version 1.4: 2015-04-29
    Changes: Database references