4V4H

Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of kasugamycin inhibition of translation.

Schuwirth, B.S.Day, J.M.Hau, C.W.Janssen, G.R.Dahlberg, A.E.Cate, J.H.D.Vila-Sanjurjo, A.

(2006) Nat Struct Mol Biol 13: 879-886

  • DOI: 10.1038/nsmb1150
  • Primary Citation of Related Structures:  
    4V4H

  • PubMed Abstract: 
  • The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance ...

    The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites).


    Organizational Affiliation

    Departments of Molecular and Cell Biology and Chemistry, University of California, Berkeley, California 94720, USA.



Macromolecules

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Entity ID: 2
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30S RIBOSOMAL PROTEIN S3 ACCC233Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S4 ADCD206Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S5 AECE167Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S6 AFCF135Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S7 AGCG179Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S8 AHCH130Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S9 AICI130Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S10 AJCJ103Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S11 AKCK129Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S12 ALCL124Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S13 AMCM118Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S14 ANCN101Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S15 AOCO89Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S16 APCP82Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S17 AQCQ84Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S18 ARCR75Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S19 ASCS92Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S20 ATCT87Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S2 ABCB241Escherichia coliMutation(s): 0 
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30S RIBOSOMAL PROTEIN S21 AUCU71Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L25 BVDV94Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L2 BCDC273Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L3 BDDD209Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L4 BEDE201Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L5 BFDF179Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L6 BGDG177Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L9 BHDH149Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L13 BJDJ142Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L14 BKDK123Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L15 BLDL144Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L16 BMDM136Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L17 BNDN127Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L18 BODO117Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L19 BPDP115Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L20 BQDQ118Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L21 BRDR103Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L22 BSDS110Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L23 BTDT100Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L24 BUDU104Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L27 BWDW85Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L29 BXDX63Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L30 BYDY59Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L31 BZDZ70Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L32 B0D057Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L33 B1D155Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L34 B2D246Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L35 B3D365Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L36 B4D438Escherichia coliMutation(s): 0 
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50S RIBOSOMAL PROTEIN L11 BIDI142Escherichia coliMutation(s): 0 
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16S RIBOSOMAL RNAAA, CA1542Escherichia coli
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5S RIBOSOMAL RNABA, DA120Escherichia coli
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MoleculeChainsLengthOrganismImage
23S RIBOSOMAL RNABB, DB2904Escherichia coli
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KSG
Query on KSG

Download Ideal Coordinates CCD File 
AA, CA
(1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE
C14 H25 N3 O9
PVTHJAPFENJVNC-MHRBZPPQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA, BB, CA, DB, DE, DN
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.331 
  • R-Value Work: 0.279 
  • R-Value Observed: 0.279 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.848α = 90
b = 379.202β = 90
c = 739.283γ = 90
Software Package:
Software NamePurpose
PHASERphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other