1OLN

Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE 

  • Method: THEORETICAL MODEL

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural Basis for Contrasting Activities of Ribosome Binding Thiazole Antibiotics

Lentzen, G.Klinck, R.Matassova, N.Aboul-Ela, F.Murchie, A.I.H.

(2003) Chem Biol 10: 769

  • DOI: 10.1016/s1074-5521(03)00173-x
  • Primary Citation of Related Structures:  
    1OLN

  • PubMed Abstract: 
  • Thiostrepton and micrococcin inhibit protein synthesis by binding to the L11 binding domain (L11BD) of 23S ribosomal RNA. The two compounds are structurally related, yet they produce different effects on ribosomal RNA in footprinting experiments and on elongation factor-G (EF-G)-dependent GTP hydrolysis ...

    Thiostrepton and micrococcin inhibit protein synthesis by binding to the L11 binding domain (L11BD) of 23S ribosomal RNA. The two compounds are structurally related, yet they produce different effects on ribosomal RNA in footprinting experiments and on elongation factor-G (EF-G)-dependent GTP hydrolysis. Using NMR and an assay based on A1067 methylation by thiostrepton-resistance methyltransferase, we show that the related thiazoles, nosiheptide and siomycin, also bind to this region. The effect of all four antibiotics on EF-G-dependent GTP hydrolysis and EF-G-GDP-ribosome complex formation was studied. Our NMR and biochemical data demonstrate that thiostrepton, nosiheptide, and siomycin share a common profile, which differs from that of micrococcin. We have generated a three-dimensional (3D) model for the interaction of thiostrepton with L11BD RNA. The model rationalizes the differences between micrococcin and the thiostrepton-like antibiotics interacting with L11BD.


    Related Citations: 
    • A Detailed View of a Ribosomal Active Site: The Structure of the L11-RNA Complex
      Wimberly, B.T., Guymon, R., Mccutcheon, J.P., White, S.W., Ramakrishnan, V.
      (1999) Cell 97: 491
    • Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
      Conn, G.L., Draper, D.E., Lattman, E.E., Gittis, A.G.
      (1999) Science 284: 1171

    Organizational Affiliation

    RiboTargets, Ltd., Granta Park, Abington, CB1 6GB, Cambridge, United Kingdom.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11A140Thermotoga maritimaMutation(s): 0 
UniProt
Find proteins for P29395 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore P29395 
Go to UniProtKB:  P29395
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29395
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
THIOSTREPTONB19Streptomyces azureusMutation(s): 0 
Gene Names: tpdA
UniProt
Find proteins for P0C8P8 (Streptomyces azureus)
Explore P0C8P8 
Go to UniProtKB:  P0C8P8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C8P8
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
RNAC 58Thermotoga maritima
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
BB9
Query on BB9
B PEPTIDE LINKINGC3 H5 N O2 SCYS
DBU
Query on DBU
B PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
B PEPTIDE LINKINGC3 H5 N O2SER
MH6
Query on MH6
B PEPTIDE LINKINGC3 H5 N O3SER
TS9
Query on TS9
B L-PEPTIDE LINKINGC6 H13 N O4ILE
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000223
Query on PRD_000223
BTHIOSTREPTONThiopeptide / Antibiotic Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • Selection Criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE 
  • OLDERADO: 1OLN Olderado
  • Method: THEORETICAL MODEL

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 1.3: 2017-11-15
    Changes: Database references
  • Version 2.0: 2019-04-24
    Changes: Data collection, Derived calculations, Polymer sequence
  • Version 2.1: 2019-08-21
    Changes: Data collection