3DLL

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

Wilson, D.N.Schluenzen, F.Harms, J.M.Starosta, A.L.Connell, S.R.Fucini, P.

(2008) Proc Natl Acad Sci U S A 105: 13339-13344

  • DOI: 10.1073/pnas.0804276105
  • Primary Citation of Related Structures:  
    3DLL

  • PubMed Abstract: 
  • The oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. We have determined the crystal structure of the oxazol ...

    The oxazolidinones represent the first new class of antibiotics to enter into clinical usage within the past 30 years, but their binding site and mechanism of action has not been fully characterized. We have determined the crystal structure of the oxazolidinone linezolid bound to the Deinococcus radiodurans 50S ribosomal subunit. Linezolid binds in the A site pocket at the peptidyltransferase center of the ribosome overlapping the aminoacyl moiety of an A-site bound tRNA as well as many clinically important antibiotics. Binding of linezolid stabilizes a distinct conformation of the universally conserved 23S rRNA nucleotide U2585 that would be nonproductive for peptide bond formation. In conjunction with available biochemical data, we present a model whereby oxazolidinones impart their inhibitory effect by perturbing the correct positioning of tRNAs on the ribosome.


    Organizational Affiliation

    Gene Center and Department of Chemistry and Biochemistry and Munich Centre for Integrated Protein Science, University of Munich, Feodor Lynen Strasse 25, 81377 Munich, Germany. wilson@lmb.uni-muenchen.de



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2 A274Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 4
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50S ribosomal protein L3 B211Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXK2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 5
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50S ribosomal protein L4 C205Deinococcus radioduransMutation(s): 0 
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Entity ID: 6
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50S ribosomal protein L5 D180Deinococcus radioduransMutation(s): 0 
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Entity ID: 7
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50S ribosomal protein L6 E185Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSL3 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 8
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50S ribosomal protein L11 F144Deinococcus radioduransMutation(s): 0 
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Entity ID: 9
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50S ribosomal protein L13 G174Deinococcus radioduransMutation(s): 0 
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Entity ID: 10
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50S ribosomal protein L14 H134Deinococcus radioduransMutation(s): 0 
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Entity ID: 11
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50S ribosomal protein L15 I156Deinococcus radioduransMutation(s): 0 
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Entity ID: 12
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50S ribosomal protein L16 J142Deinococcus radioduransMutation(s): 0 
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Entity ID: 13
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50S ribosomal protein L17 K116Deinococcus radioduransMutation(s): 0 
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Entity ID: 14
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50S ribosomal protein L18 L114Deinococcus radioduransMutation(s): 0 
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Entity ID: 15
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50S ribosomal protein L19 M166Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RWB4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 16
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50S ribosomal protein L20 N118Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSW7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 17
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50S ribosomal protein L21 O100Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RY64 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 18
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50S ribosomal protein L22 P134Deinococcus radioduransMutation(s): 0 
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Entity ID: 19
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50S ribosomal protein L23 Q95Deinococcus radioduransMutation(s): 0 
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Entity ID: 20
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50S ribosomal protein L24 R115Deinococcus radioduransMutation(s): 0 
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Entity ID: 21
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50S ribosomal protein L25 S237Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RX88 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 22
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50S ribosomal protein L27 T91Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RY65 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 23
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50S ribosomal protein L28 U81Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RRG8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 24
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50S ribosomal protein L29 V67Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RXJ4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30 W55Deinococcus radioduransMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32 Y60Deinococcus radioduransMutation(s): 0 
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33 155Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSS4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34 247Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSH2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35 366Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSW6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36 437Deinococcus radioduransMutation(s): 0 
Find proteins for Q9RSK0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
rRNA-23S ribosomal RNAX2880Deinococcus radiodurans
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Entity ID: 2
MoleculeChainsLengthOrganismImage
rRNA-5S ribosomal RNAZ123Deinococcus radiodurans
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZLD
Query on ZLD

Download Ideal Coordinates CCD File 
X
N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide
C16 H20 F N3 O4
TYZROVQLWOKYKF-ZDUSSCGKSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
4, Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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M, X, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.259 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.7α = 90
b = 410β = 90
c = 695γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2009-02-24
    Changes: Version format compliance
  • Version 1.2: 2015-06-17
    Changes: Version format compliance
  • Version 1.3: 2015-07-08
    Changes: Other
  • Version 1.4: 2015-07-22
    Changes: Non-polymer description, Other