4U27

Crystal structure of the E. coli ribosome bound to flopristin and linopristin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2AB, CB218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3AC, CC206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4AD, CD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6AF, CF100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7AG, CG151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8AH, CH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9AI, CI127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 10
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30S ribosomal protein S10AJ, CJ98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 11
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30S ribosomal protein S11AK, CK117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12AL, CL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13AM, CM114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14AN, CN100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16AP, CP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17AQ, CQ80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 19
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30S ribosomal protein S19AS, CS79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20AT, CT85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21AU, CU51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2BC, DC271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3BD, DD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4BE, DE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5BF, DF177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6BG, DG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9BH, DH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11BI, DI141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15BL, DL143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16BM, DM136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17BN, DN120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18BO, DO116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19BP, DP114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22BS, DS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23BT, DT93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24BU, DU102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25BV, DV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27BW, DW76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28BX, DX77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29BY, DY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30BZ, DZ58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32B0, D056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33B1, D150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 50
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50S ribosomal protein L34B2, D246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 51
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50S ribosomal protein L35B3, D364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 52
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50S ribosomal protein L36B4, D438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1B5228Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
LinopristinB6, D67synthetic constructMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15AO, CO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18AR, CR55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13BJ, DJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14BK, DK122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20BQ, DQ117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21BR, DR103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5AE, CE150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 22
MoleculeChainsLengthOrganism
23S rRNABA, DA2903Escherichia coli str. K-12 substr. MDS42

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Entity ID: 23
MoleculeChainsLengthOrganism
5S rRNABB, DB119Escherichia coli str. K-12 substr. MDS42

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Entity ID: 1
MoleculeChainsLengthOrganism
16S rRNAAA, CA1539Escherichia coli str. K-12 substr. MDS42
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VIF
Query on VIF

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BA, DA
Flopristin
C28 H38 F N3 O6
DFSJQGCLWZVMOD-IQIMCDJDSA-N
 Ligand Interaction
ZN
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B4, D4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
AA, BA, BB, BD, BQ, CA, D2, DA, DB
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002101
Query on PRD_002101
B6, D6LinopristinP /  Antibiotic

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MHU
Query on MHU
B6,D6L-PEPTIDE LINKINGC12 H18 N2 O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.97α = 90
b = 434.65β = 90
c = 623.91γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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