5J7L

Structure of the 70S E coli ribosome with the U1052G mutation in the 16S rRNA bound to tetracycline

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report



Literature

Resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.

Cocozaki, A.I., Altman, R.B., Huang, J., Buurman, E.T., Kazmirski, S.L., Doig, P., Prince, D.B., Blanchard, S.C., Cate, J.H., Ferguson, A.D.

(2016) Proc Natl Acad Sci U S A 113: 8188-8193

  • DOI: 10.1073/pnas.1605127113
  • Primary Citation of Related Structures:  
    5IT8, 5J5B, 5J8A, 5J88, 5J7L, 5J91, 5JC9

  • PubMed Abstract: 

    • Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly re ...

    Mutations conferring resistance to translation inhibitors often alter the structure of rRNA. Reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. The translation inhibitors negamycin and tetracycline interfere with tRNA binding to the aminoacyl-tRNA site on the small 30S ribosomal subunit. However, two negamycin resistance mutations display unexpected differential antibiotic susceptibility profiles. Mutant U1060A in 16S Escherichia coli rRNA is resistant to both antibiotics, whereas mutant U1052G is simultaneously resistant to negamycin and hypersusceptible to tetracycline. Using a combination of microbiological, biochemical, single-molecule fluorescence transfer experiments, and X-ray crystallography, we define the specific structural defects in the U1052G mutant 70S E. coli ribosome that explain its divergent negamycin and tetracycline susceptibility profiles. Unexpectedly, the U1052G mutant ribosome possesses a second tetracycline binding site that correlates with its hypersusceptibility. The creation of a previously unidentified antibiotic binding site raises the prospect of identifying similar phenomena in antibiotic-resistant pathogens in the future.

    Organizational Affiliation: 

    Structure and Biophysics, Discovery Sciences, AstraZeneca Pharmaceuticals, Waltham, MA 02451; Andrew.Ferguson@astrazeneca.com.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2 AB, BB224Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsB, b0169, JW0164
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Entity ID: 3
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30S ribosomal protein S3 AC, BC206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsC, b3314, JW3276
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Entity ID: 4
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30S ribosomal protein S4 AD, BD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsD, ramA, b3296, JW3258
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Entity ID: 5
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30S ribosomal protein S5 AE, BE155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsE, spc, b3303, JW3265
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Entity ID: 6
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30S ribosomal protein S6 AF, BF106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsF, b4200, JW4158
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Entity ID: 7
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30S ribosomal protein S7 AG, BG151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsG, b3341, JW3303
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30S ribosomal protein S8 AH, BH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsH, b3306, JW3268
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30S ribosomal protein S9 AI, BI127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsI, b3230, JW3199
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30S ribosomal protein S10 AJ, BJ99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJ, nusE, b3321, JW3283
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30S ribosomal protein S11 AK, BK117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsK, b3297, JW3259
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30S ribosomal protein S12 AL, BL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsL, strA, b3342, JW3304
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30S ribosomal protein S13 AM, BM114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsM, b3298, JW3260
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30S ribosomal protein S14 AN, BN100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsN, b3307, JW3269
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30S ribosomal protein S15 AO, BO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsO, secC, b3165, JW3134
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30S ribosomal protein S16 AP, BP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsP, b2609, JW2590
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30S ribosomal protein S17 AQ, BQ80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQ, neaA, b3311, JW3273
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30S ribosomal protein S18 AR, BR55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsR, b4202, JW4160
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30S ribosomal protein S19 AS, BS79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsS, b3316, JW3278
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30S ribosomal protein S20 AT, BT86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsT, b0023, JW0022
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30S ribosomal protein S21 AU, BU56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsU, b3065, JW3037
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50S ribosomal protein L32 C1, D156Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmF, b1089, JW1075
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50S ribosomal protein L33 C2, D251Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmG, b3636, JW3611
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50S ribosomal protein L34 C3, D346Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmH, rimA, ssaF, b3703, JW3680
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50S ribosomal protein L35 C4, D464Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmI, b1717, JW1707
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50S ribosomal protein L36 C5, D538Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJ, b3299, JW3261
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50S ribosomal protein L30 C0, D058Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmD, b3302, JW3264
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50S ribosomal protein L2 CC, DC271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplB, b3317, JW3279
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50S ribosomal protein L3 CD, DD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplC, b3320, JW3282
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50S ribosomal protein L4 CE, DE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplD, eryA, b3319, JW3281
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50S ribosomal protein L5 CF, DF177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplE, b3308, JW3270
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50S ribosomal protein L6 CG, DG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplF, b3305, JW3267
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50S ribosomal protein L9 CH, DH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplI, b4203, JW4161
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50S ribosomal protein L11 CJ, DJ134Escherichia coli K-12Mutation(s): 0 
Gene Names: rplK, relC, b3983, JW3946
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50S ribosomal protein L13 CK, DK142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplM, b3231, JW3200
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50S ribosomal protein L14 CL, DL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplN, b3310, JW3272
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50S ribosomal protein L15 CM, DM144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplO, b3301, JW3263
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50S ribosomal protein L16 CN, DN136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplP, b3313, JW3275
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50S ribosomal protein L17 CO, DO125Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQ, b3294, JW3256
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50S ribosomal protein L18 CP, DP117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplR, b3304, JW3266
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50S ribosomal protein L19 CQ, DQ114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplS, b2606, JW2587
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50S ribosomal protein L20 CR, DR117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplT, pdzA, b1716, JW1706
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50S ribosomal protein L21 CS, DS103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplU, b3186, JW3153
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50S ribosomal protein L22 CT, DT110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplV, eryB, b3315, JW3277
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50S ribosomal protein L23 CU, DU93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplW, b3318, JW3280
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50S ribosomal protein L24 CV, DV102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplX, b3309, JW3271
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50S ribosomal protein L25 CW, DW94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplY, b2185, JW2173
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50S ribosomal protein L27 CX, DX76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmA, b3185, JW3152
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50S ribosomal protein L28 CY, DY77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmB, b3637, JW3612
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50S ribosomal protein L29 CZ, DZ62Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmC, b3312, JW3274
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50S ribosomal protein L10 DI135Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJ, b3985, JW3948
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16S rRNAAA, BA1534Escherichia coli K-12
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23S rRNACA2904Escherichia coli K-12
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23S rRNADA2904Escherichia coli K-12
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAC
Query on TAC
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AA, BA
TETRACYCLINE
C22 H24 N2 O8
OFVLGDICTFRJMM-WESIUVDSSA-N		 Ligand Interaction
1PE
Query on 1PE
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DA
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
AA, BA, DA, DQ, DR, DS
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
GUN
Query on GUN
Download Ideal Coordinates CCD File 
DA
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
D1, DA, DS, DU
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
SPD
Query on SPD
Download Ideal Coordinates CCD File 
DA
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
DA
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
AA, DA, DE, DK, DN, DS, DT
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
AL, D1, D3, DA, DL, DP, DQ
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
PUT
Query on PUT
Download Ideal Coordinates CCD File 
AA, DA, DM
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AB, C5, D5
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
D1, DA, DB
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
ACY
Query on ACY
Download Ideal Coordinates CCD File 
DA
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
AA, BA, CA, CB, DA, DB, DD, DM, DR
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
D2T
Query on D2T		AL,BLL-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ		CD,DDL-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4		CN,DNL-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.41α = 90
b = 435.7β = 90
c = 625.25γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Changes: Database references
  • Version 1.2: 2017-05-31
    Changes: Structure summary
  • Version 2.0: 2018-08-01
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 3.0: 2018-08-15
    Changes: Atomic model, Data collection