Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.48 kDa 
• Atom Count: 2350 
• Modelled Residue Count: 210 
• Deposited 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

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

• Classification: RIBOSOME/ANTIBIOTIC
• Organism(s): Thermotoga maritima, Streptomyces azureus
• Mutation(s): No 


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

---

Experimental Data Snapshot

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

---

• Method: THEORETICAL MODEL

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 
• 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. 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

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

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

Small Molecules

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BB9	B	PEPTIDE LINKING	C3 H5 N O2 S		CYS
DBU	B	PEPTIDE LINKING	C4 H7 N O2		THR
DHA	B	PEPTIDE LINKING	C3 H5 N O2		SER
MH6	B	PEPTIDE LINKING	C3 H5 N O3		SER
TS9	B	L-PEPTIDE LINKING	C6 H13 N O4		ILE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000223	B	THIOSTREPTON	Thiopeptide / Antibiotic		Ligand Interaction

Experimental Data & Validation

Experimental Data

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

• Method: THEORETICAL MODEL

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
  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