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- PDB-1oln: Model for thiostrepton antibiotic binding to L11 substrate from 5... -
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Basic information
Entry | Database: PDB / ID: 1oln | |||||||||
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Title | Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA | |||||||||
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![]() | RIBOSOME/ANTIBIOTIC / RIBOSOME-ANTIBIOTIC COMPLEX / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / OXAZOLE / RIBOSOME / L11 / TRANSLATION INHIBITION | |||||||||
Function / homology | ![]() large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / defense response to bacterium / translation / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | SOLUTION NMR / THEORETICAL MODEL / DOCKING, MODELING | |||||||||
Model type details | MINIMIZED AVERAGE | |||||||||
![]() | Lentzen, G. / Klinck, R. / Matassova, N. / Aboul-Ela, F. / Murchie, A.I.H. | |||||||||
![]() | ![]() Title: Structural Basis for Contrasting Activities of Ribosome Binding Thiazole Antibiotics Authors: Lentzen, G. / Klinck, R. / Matassova, N. / Aboul-Ela, F. / Murchie, A.I.H. #1: ![]() Title: A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Authors: B T Wimberly / R Guymon / J P McCutcheon / S W White / V Ramakrishnan / ![]() Abstract: We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton ...We report the crystal structure of a 58 nucleotide fragment of 23S ribosomal RNA bound to ribosomal protein L11. This highly conserved ribonucleoprotein domain is the target for the thiostrepton family of antibiotics that disrupt elongation factor function. The highly compact RNA has both familiar and novel structural motifs. While the C-terminal domain of L11 binds RNA tightly, the N-terminal domain makes only limited contacts with RNA and is proposed to function as a switch that reversibly associates with an adjacent region of RNA. The sites of mutations conferring resistance to thiostrepton and micrococcin line a narrow cleft between the RNA and the N-terminal domain. These antibiotics are proposed to bind in this cleft, locking the putative switch and interfering with the function of elongation factors. #2: ![]() Title: Crystal Structure of a Conserved Ribosomal Protein-RNA Complex Authors: Conn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G. | |||||||||
History |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
-Experimental details
-Experiment
Experiment |
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NMR experiment | Type: NOESY | |||
NMR details | Text: BEST OVERALL DOCKING SCORE AND LEAST RESTRAINT VIOLATION. THE NOES INCLUDED IN THE RESTRAINTED MODELING WERE OBTAINED FROM A FILTERED NOESY EXPERIMENT ON A COMPLEX OF UNLABELED THIOSTREPTON ...Text: BEST OVERALL DOCKING SCORE AND LEAST RESTRAINT VIOLATION. THE NOES INCLUDED IN THE RESTRAINTED MODELING WERE OBTAINED FROM A FILTERED NOESY EXPERIMENT ON A COMPLEX OF UNLABELED THIOSTREPTON WITH THE RNA. AS ALL INTERNAL COORDINATES WERE HELD RIGID ACCORDING TO THE X-RAY STRUCTURES, ONLY INTERMOLECULAR NOES WERE INCLUDED. ASSIGNMENTS FOR RNA WERE CHOSEN FROM AN ITERATIVE DOCKING PROCESS (SEE LENTZEN ET AL AND MANUSCRIPT TO BE PUBLISHED) |
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Sample preparation
Sample conditions | Ionic strength: 100 MM NACL, 5 MM MGCL2 / pH: 6.2 / Pressure: 1 atm / Temperature: 303 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-Data collection
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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Processing
NMR software | Name: rDOCK / Developer: DAVID MORLEY / Classification: refinement |
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Refinement | Method: DOCKING, MODELING / Software ordinal: 1 Details: THE COORDINATES OF THE PROTEIN, RNA AND THE ANTIBIOTIC WERE HELD RIGID DURING REFINEMENT. THE COORDINATES OF THE RIBOSOMAL L11 (CHAIN A) AND THE RNA (CHAIN C) WERE FROM PDB ENTRY 1MMS. THE ...Details: THE COORDINATES OF THE PROTEIN, RNA AND THE ANTIBIOTIC WERE HELD RIGID DURING REFINEMENT. THE COORDINATES OF THE RIBOSOMAL L11 (CHAIN A) AND THE RNA (CHAIN C) WERE FROM PDB ENTRY 1MMS. THE COORDINATES OF THE ANTIBIOTIC THIOSTREPTON (CHAIN B) WERE FROM PDB ENTRY 1E9W. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION. |
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE Conformers submitted total number: 1 |