2JQ7

Model for thiostrepton binding to the ribosomal L11-RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: TOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history

Literature

L11 Domain Rearrangement Upon Binding to RNA and Thiostrepton Studied by NMR Spectroscopy

Jonker, H.R.A.Ilin, S.Grimm, S.K.Woehnert, J.Schwalbe, H.

(2007) Nucleic Acids Res. 35: 441

  • DOI: 10.1093/nar/gkl1066
  • Primary Citation of Related Structures:  
  • Also Cited By: 2K3F

  • PubMed Abstract: 
  • Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have s ...

    Ribosomal proteins are assumed to stabilize specific RNA structures and promote compact folding of the large rRNA. The conformational dynamics of the protein between the bound and unbound state play an important role in the binding process. We have studied those dynamical changes in detail for the highly conserved complex between the ribosomal protein L11 and the GTPase region of 23S rRNA. The RNA domain is compactly folded into a well defined tertiary structure, which is further stabilized by the association with the C-terminal domain of the L11 protein (L11(ctd)). In addition, the N-terminal domain of L11 (L11(ntd)) is implicated in the binding of the natural thiazole antibiotic thiostrepton, which disrupts the elongation factor function. We have studied the conformation of the ribosomal protein and its dynamics by NMR in the unbound state, the RNA bound state and in the ternary complex with the RNA and thiostrepton. Our data reveal a rearrangement of the L11(ntd), placing it closer to the RNA after binding of thiostrepton, which may prevent binding of elongation factors. We propose a model for the ternary L11-RNA-thiostrepton complex that is additionally based on interaction data and conformational information of the L11 protein. The model is consistent with earlier findings and provides an explanation for the role of L11(ntd) in elongation factor binding.


    Organizational Affiliation

    Johann Wolfgang Goethe-University, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
A
141Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: rplK
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  P29395
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THIOSTREPTON
C
19Streptomyces azureusMutation(s): 0 
Gene Names: tpdA
Find proteins for P0C8P8 (Streptomyces azureus)
Go to UniProtKB:  P0C8P8
Entity ID: 2
MoleculeChainsLengthOrganism
RIBOSOMAL RNAB58Escherichia coli
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000223
Query on PRD_000223
CTHIOSTREPTONThiopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 10 
  • Selection Criteria: TOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other
  • Version 1.5: 2015-05-27
    Type: Source and taxonomy
  • Version 1.6: 2017-11-01
    Type: Derived calculations, Structure summary