4WF1

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome.

Olivier, N.B.Altman, R.B.Noeske, J.Basarab, G.S.Code, E.Ferguson, A.D.Gao, N.Huang, J.Juette, M.F.Livchak, S.Miller, M.D.Prince, D.B.Cate, J.H.Buurman, E.T.Blanchard, S.C.

(2014) Proc Natl Acad Sci U S A 111: 16274-16279

  • DOI: 10.1073/pnas.1414401111
  • Primary Citation of Related Structures:  
    4WF1

  • PubMed Abstract: 
  • Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell dea ...

    Negamycin is a natural product with broad-spectrum antibacterial activity and efficacy in animal models of infection. Although its precise mechanism of action has yet to be delineated, negamycin inhibits cellular protein synthesis and causes cell death. Here, we show that single point mutations within 16S rRNA that confer resistance to negamycin are in close proximity of the tetracycline binding site within helix 34 of the small subunit head domain. As expected from its direct interaction with this region of the ribosome, negamycin was shown to displace tetracycline. However, in contrast to tetracycline-class antibiotics, which serve to prevent cognate tRNA from entering the translating ribosome, single-molecule fluorescence resonance energy transfer investigations revealed that negamycin specifically stabilizes near-cognate ternary complexes within the A site during the normally transient initial selection process to promote miscoding. The crystal structure of the 70S ribosome in complex with negamycin, determined at 3.1 Å resolution, sheds light on this finding by showing that negamycin occupies a site that partially overlaps that of tetracycline-class antibiotics. Collectively, these data suggest that the small subunit head domain contributes to the decoding mechanism and that small-molecule binding to this domain may either prevent or promote tRNA entry by altering the initial selection mechanism after codon recognition and before GTPase activation.


    Organizational Affiliation

    Department of Physiology and Biophysics & the Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medical College, New York, NY 10065; scb2005@med.cornell.edu Ed.Buurman@astrazeneca.com.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S2ABCB218Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsBb0169JW0164
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Entity ID: 3
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30S ribosomal protein S3ACCC206Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsCb3314JW3276
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Entity ID: 4
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30S ribosomal protein S4ADCD205Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsDramAb3296JW3258
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Entity ID: 5
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30S ribosomal protein S5AECE150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsEspcb3303JW3265
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Entity ID: 6
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30S ribosomal protein S6AFCF100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 7
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30S ribosomal protein S7AGCG151Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 8
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30S ribosomal protein S8AHCH129Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsHb3306JW3268
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Entity ID: 9
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30S ribosomal protein S9AICI127Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsIb3230JW3199
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Entity ID: 10
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30S ribosomal protein S10AJCJ98Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsJnusEb3321JW3283
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Entity ID: 11
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30S ribosomal protein S11AKCK117Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsKb3297JW3259
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Entity ID: 12
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30S ribosomal protein S12ALCL123Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsLstrAb3342JW3304
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Entity ID: 13
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30S ribosomal protein S13AMCM114Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsMb3298JW3260
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Entity ID: 14
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30S ribosomal protein S14ANCN100Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsNb3307JW3269
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Entity ID: 15
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30S ribosomal protein S15AOCO88Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
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Entity ID: 16
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30S ribosomal protein S16APCP82Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsPb2609JW2590
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Entity ID: 17
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30S ribosomal protein S17AQCQ80Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
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Entity ID: 18
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30S ribosomal protein S18ARCR55Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsRb4202JW4160
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Entity ID: 19
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30S ribosomal protein S19ASCS79Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsSb3316JW3278
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Entity ID: 20
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30S ribosomal protein S20ATCT85Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsTb0023JW0022
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Entity ID: 21
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30S ribosomal protein S21AUCU51Escherichia coli K-12Mutation(s): 0 
Gene Names: rpsUb3065JW3037
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Entity ID: 24
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50S ribosomal protein L2BCDC271Escherichia coli K-12Mutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 25
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50S ribosomal protein L3BDDD209Escherichia coli K-12Mutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 26
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50S ribosomal protein L4BEDE201Escherichia coli K-12Mutation(s): 0 
Gene Names: rplDeryAb3319JW3281
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Entity ID: 27
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50S ribosomal protein L5BFDF177Escherichia coli K-12Mutation(s): 0 
Gene Names: rplEb3308JW3270
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Entity ID: 28
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50S ribosomal protein L6BGDG176Escherichia coli K-12Mutation(s): 0 
Gene Names: rplFb3305JW3267
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Entity ID: 29
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50S ribosomal protein L9BHDH149Escherichia coli K-12Mutation(s): 0 
Gene Names: rplIb4203JW4161
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Entity ID: 30
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50S ribosomal protein L11BIDI141Escherichia coli K-12Mutation(s): 0 
Gene Names: rplKrelCb3983JW3946
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Entity ID: 31
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50S ribosomal protein L13BJDJ142Escherichia coli K-12Mutation(s): 0 
Gene Names: rplMb3231JW3200
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Entity ID: 32
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50S ribosomal protein L14BKDK122Escherichia coli K-12Mutation(s): 0 
Gene Names: rplNb3310JW3272
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Entity ID: 33
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50S ribosomal protein L15BLDL143Escherichia coli K-12Mutation(s): 0 
Gene Names: rplOb3301JW3263
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Entity ID: 34
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50S ribosomal protein L16BMDM136Escherichia coli K-12Mutation(s): 0 
Gene Names: rplPb3313JW3275
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Entity ID: 35
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50S ribosomal protein L17BNDN120Escherichia coli K-12Mutation(s): 0 
Gene Names: rplQb3294JW3256
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Entity ID: 36
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50S ribosomal protein L18BODO116Escherichia coli K-12Mutation(s): 0 
Gene Names: rplRb3304JW3266
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Entity ID: 37
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50S ribosomal protein L19BPDP114Escherichia coli K-12Mutation(s): 0 
Gene Names: rplSb2606JW2587
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Entity ID: 38
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50S ribosomal protein L20BQDQ117Escherichia coli K-12Mutation(s): 0 
Gene Names: rplTpdzAb1716JW1706
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Entity ID: 39
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50S ribosomal protein L21BRDR103Escherichia coli K-12Mutation(s): 0 
Gene Names: rplUb3186JW3153
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Entity ID: 40
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50S ribosomal protein L22BSDS110Escherichia coli K-12Mutation(s): 0 
Gene Names: rplVeryBb3315JW3277
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Entity ID: 41
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50S ribosomal protein L23BTDT93Escherichia coli K-12Mutation(s): 0 
Gene Names: rplWb3318JW3280
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Entity ID: 42
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50S ribosomal protein L24BUDU102Escherichia coli K-12Mutation(s): 0 
Gene Names: rplXb3309JW3271
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Entity ID: 43
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50S ribosomal protein L25BVDV94Escherichia coli K-12Mutation(s): 0 
Gene Names: rplYb2185JW2173
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Entity ID: 44
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50S ribosomal protein L27BWDW76Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 45
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50S ribosomal protein L28BXDX77Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmBb3637JW3612
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Entity ID: 46
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50S ribosomal protein L29BYDY63Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmCb3312JW3274
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Entity ID: 47
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50S ribosomal protein L30BZDZ58Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmDb3302JW3264
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Entity ID: 48
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50S ribosomal protein L32B0D056Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmFb1089JW1075
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Entity ID: 49
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50S ribosomal protein L33B1D150Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmGb3636JW3611
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Entity ID: 50
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50S ribosomal protein L34B2D246Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmHrimAssaFb3703JW3680
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Entity ID: 51
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50S ribosomal protein L35B3D364Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmIb1717JW1707
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 52
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50S ribosomal protein L36B4D438Escherichia coli K-12Mutation(s): 0 
Gene Names: rpmJb3299JW3261
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 53
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50S ribosomal protein L1B5207Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplATTHA0246
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Go to UniProtKB:  Q5SLP7
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
16S rRNAAA, CA1539Escherichia coli str. K-12 substr. MG1655
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(by identity cutoff)  |  Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
23S rRNABA, DA2903Escherichia coli str. K-12 substr. MG1655
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(by identity cutoff)  |  Structure
Entity ID: 23
MoleculeChainsLengthOrganismImage
5S rRNABB, DB119Escherichia coli str. K-12 substr. MG1655
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NEG
Query on NEG

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CA
NEGAMYCIN
C9 H20 N4 O4
IKHFJPZQZVMLRH-RNFRBKRXSA-N
 Ligand Interaction
ZN
Query on ZN

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B4, D4
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AA, AM, BA, BB, BQ, CA, CT, D2, DA, DB, DL, DQ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.91α = 90
b = 434.31β = 90
c = 624.4γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2017-11-22
    Changes: Advisory, Database references, Derived calculations, Refinement description, Source and taxonomy