5J91

Structure of the Wild-type 70S E coli ribosome bound to Tigecycline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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:  
    5J5B, 5J8A, 5J88, 5J7L, 5J91, 5JC9, 5IT8

  • 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 significantl ...

    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 S2ABBB224Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 3
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30S ribosomal protein S3ACBC206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 4
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30S ribosomal protein S4ADBD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 6
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30S ribosomal protein S6AFBF106Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 7
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30S ribosomal protein S7AGBG151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 8
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30S ribosomal protein S8AHBH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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30S ribosomal protein S9AIBI127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 10
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30S ribosomal protein S10AJBJ99Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 12
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30S ribosomal protein S12ALBL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 13
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30S ribosomal protein S13AMBM114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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30S ribosomal protein S15AOBO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 16
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30S ribosomal protein S16APBP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 18
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30S ribosomal protein S18ARBR55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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30S ribosomal protein S19ASBS79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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30S ribosomal protein S20ATBT86Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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30S ribosomal protein S21AUBU56Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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50S ribosomal protein L32C1D156Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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50S ribosomal protein L33C2D251Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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50S ribosomal protein L34C3D346Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 25
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50S ribosomal protein L35C4D464Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
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Entity ID: 29
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50S ribosomal protein L2CCDC272Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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50S ribosomal protein L3CD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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50S ribosomal protein L5CFDF178Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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50S ribosomal protein L6CGDG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 37
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50S ribosomal protein L11CJDJ134Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 40
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50S ribosomal protein L15CMDM144Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 42
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50S ribosomal protein L17CODO125Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 44
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50S ribosomal protein L19CQDQ114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 45
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50S ribosomal protein L20CRDR117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 46
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50S ribosomal protein L21CSDS103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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50S ribosomal protein L22CTDT110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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50S ribosomal protein L23CUDU93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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50S ribosomal protein L24CVDV103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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50S ribosomal protein L25CWDW94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 51
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50S ribosomal protein L27CXDX76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 53
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50S ribosomal protein L29CZDZ62Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 54
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50S ribosomal protein L10DI135Escherichia coli K-12Mutation(s): 0 
Gene Names: rplJb3985JW3948
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Entity ID: 11
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30S ribosomal protein S11AKBK117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 14
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30S ribosomal protein S14ANBN100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 17
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30S ribosomal protein S17AQBQ80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 26
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50S ribosomal protein L36C5D538Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
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Entity ID: 27
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50S ribosomal protein L30C0D058Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 32
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50S ribosomal protein L3DD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 33
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50S ribosomal protein L4CEDE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 36
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50S ribosomal protein L9CHDH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 38
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50S ribosomal protein L13CKDK142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 39
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50S ribosomal protein L14CLDL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 41
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50S ribosomal protein L16CNDN136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 43
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50S ribosomal protein L18CPDP117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 5
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30S ribosomal protein S5AEBE155Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28CYDY77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
Find proteins for P0A7M2 (Escherichia coli (strain K12))
Explore P0A7M2 
Go to UniProtKB:  P0A7M2
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAAA, BA1534Escherichia coli
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Entity ID: 31
MoleculeChainsLengthOrganismImage
23S rRNACA2904Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganismImage
23S rRNADA2904Escherichia coli K-12
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Entity ID: 28
MoleculeChainsLengthOrganismImage
5S rRNACB, DB120Escherichia coli
Small Molecules
Ligands 14 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T1C
Query on T1C

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AA, BA
TIGECYCLINE
C29 H41 N5 O8
FPZLLRFZJZRHSY-HJYUBDRYSA-P
 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

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AA, BA, DA, DQ, DR, DS
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
GUN
Query on GUN

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DA
GUANINE
C5 H5 N5 O
UYTPUPDQBNUYGX-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

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D1, D3, DA, DD, DS, DU
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
SPD
Query on SPD

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DA
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

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DA
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

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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

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AL, D1, D3, DA, DL, DP, DQ
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PUT
Query on PUT

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AA, DA
1,4-DIAMINOBUTANE
C4 H12 N2
KIDHWZJUCRJVML-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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AB, C5, D5
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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D1, DA, DB
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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DA
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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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
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: 2.96 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.18α = 90
b = 434.82β = 90
c = 624.26γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-06
    Type: Initial release
  • Version 1.1: 2016-07-20
    Changes: Structure summary
  • Version 1.2: 2016-08-03
    Changes: Database references