1OND

THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insight into the role of the ribosomal tunnel in cellular regulation

Berisio, R.Schluenzen, F.Harms, J.Bashan, A.Auerbach, T.Baram, D.Yonath, A.

(2003) Nat.Struct.Mol.Biol. 10: 366-370

  • DOI: 10.1038/nsb915

  • PubMed Abstract: 
  • Nascent proteins emerge out of ribosomes through an exit tunnel, which was assumed to be a firmly built passive path. Recent biochemical results, however, indicate that the tunnel plays an active role in sequence-specific gating of nascent chains and ...

    Nascent proteins emerge out of ribosomes through an exit tunnel, which was assumed to be a firmly built passive path. Recent biochemical results, however, indicate that the tunnel plays an active role in sequence-specific gating of nascent chains and in responding to cellular signals. Consistently, modulation of the tunnel shape, caused by the binding of the semi-synthetic macrolide troleandomycin to the large ribosomal subunit from Deinococcus radiodurans, was revealed crystallographically. The results provide insights into the tunnel dynamics at high resolution. Here we show that, in addition to the typical steric blockage of the ribosomal tunnel by macrolides, troleandomycin induces a conformational rearrangement in a wall constituent, protein L22, flipping the tip of its highly conserved beta-hairpin across the tunnel. On the basis of mutations that alleviate elongation arrest, the tunnel motion could be correlated with sequence discrimination and gating, suggesting that specific arrest motifs within nascent chain sequences may induce a similar gating mechanism.


    Related Citations: 
    • Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria
      Schlunzen, F.,Zarivach, R.,Harms, J.,Bashan, A.,Tocilj, A.,Albrecht, R.,Yonath, A.,Franceschi, F.
      (2001) Nature 413: 814


    Organizational Affiliation

    Max-Planck-Research Unit for Ribosomal Structure, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
Q
134Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: rplV
Find proteins for Q9RXJ7 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  Q9RXJ7
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
Z
60Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)Gene Names: rpmF
Find proteins for P49228 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422))
Go to UniProtKB:  P49228
Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02880Deinococcus radiodurans
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAO
Query on TAO

Download SDF File 
Download CCD File 
0
TROLEANDOMYCIN
(3R,5S,6S,7R,8S,11S,12R,13S,14R,15S)-12-[(4-O-ACETYL-2,6-DIDEOXY-3-O-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSYL)OXY]-14-{[2-O-ACETYL-3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSYL]OXY}-5,7,8,11,13,15-HEXAMETHYL-4,10-DIOXO-1,9-DIOXASPIRO[2.13]HEXADEC-6-YL ACETATE
C41 H67 N O15
LQCLVBQBTUVCEQ-CLPGKMRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.261 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 170.250α = 90.00
b = 411.090β = 90.00
c = 695.340γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CCP4model building
CCP4phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance