Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35479.86 
• Atom Count: 2350 
• Residue Count: 217 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

1OLN

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

• DOI: 10.2210/pdb1OLN/pdb
• NDB: 1OLN

• Classification: RIBOSOME/ANTIBIOTIC
• Organism(s): Thermotoga maritima, Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099), Streptomyces azureus


• Deposited: 2003-08-08 Released: 2003-09-11 
• Deposition Author(s): Lentzen, G., Klinck, R., Matassova, N., Aboul-Ela, F., Murchie, A.I.H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE 

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

• PubMed: 12954336 


• 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. 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.

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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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
50S RIBOSOMAL PROTEIN L11	A	140	Thermotoga 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: 2
Molecule	Chains	Sequence Length	Organism	Details
THIOSTREPTON	B	19	Streptomyces azureus	Mutation(s): 0  Gene Names: tpdA
Find proteins for P0C8P8 (Streptomyces azureus) Go to UniProtKB:  P0C8P8

Entity ID: 3
Molecule	Chains	Length	Organism
RNA	C	58	Thermotoga maritima

Small Molecules

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000223	B	THIOSTREPTON	Thiopeptide / Antibiotic		--

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE 

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-08 
• Released Date: 2003-09-11 
• Deposition Author(s): Lentzen, G., Klinck, R., Matassova, N., Aboul-Ela, F., Murchie, A.I.H.

Revision History 

• Version 1.0: 2003-09-11
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
• Version 1.2: 2012-11-30
  Type: Other
• Version 1.3: 2017-11-15
  Type: Database references