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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
TitleModel for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA
Components
  • 50S RIBOSOMAL PROTEIN L11
  • RNA
  • THIOSTREPTON
KeywordsRIBOSOME/ANTIBIOTIC / RIBOSOME-ANTIBIOTIC COMPLEX / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / OXAZOLE / RIBOSOME / L11 / TRANSLATION INHIBITION
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / defense response to bacterium / structural constituent of ribosome / translation / extracellular region
Similarity search - Function
Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily ...Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, RNA binding domain
Similarity search - Domain/homology
THIOSTREPTON / RNA / RNA (> 10) / Thiostrepton / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
STREPTOMYCES AZUREUS (bacteria)
MethodSOLUTION NMR / THEORETICAL MODEL / DOCKING, MODELING
Model type detailsMINIMIZED AVERAGE
AuthorsLentzen, G. / Klinck, R. / Matassova, N. / Aboul-Ela, F. / Murchie, A.I.H.
Citation
Journal: Chem.Biol. / Year: 2003
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: Journal: Cell / Year: 1999
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: Journal: Science / Year: 1999
Title: Crystal Structure of a Conserved Ribosomal Protein-RNA Complex
Authors: Conn, G.L. / Draper, D.E. / Lattman, E.E. / Gittis, A.G.
History
DepositionAug 8, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Nov 15, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 50S RIBOSOMAL PROTEIN L11
B: THIOSTREPTON
C: RNA


Theoretical massNumber of molelcules
Total (without water)35,4803
Polymers35,4803
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE
Representative

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L11


Mass: 14980.726 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOTOGA MARITIMA (bacteria) / References: UniProt: P29395
#2: Protein/peptide THIOSTREPTON / ALANINAMIDE / BRYAMYCIN / THIACTIN


Type: Thiopeptide / Class: Antibiotic / Mass: 1805.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain ...Details: Thiostrepton is a hetrocyclic thiopeptide belonging to the thiocillin family, consisting of four thiazole, one thiozoline and one piperideine rings. A modified quinoline linked to main-chain residue 1 and side-chain of residue 12. Post translational maturation of thiazole and oxazole containing antibiotics involves the enzymic condensation of a Cys or Ser with the alpha-carbonyl of the preceding amino acid to form a thioether or ether bond, then dehydration to form a double bond with the alpha-amino nitrogen. Thiazoline or oxazoline ring are dehydrogenated to form thiazole or oxazole rings. the pyridinyl involves the cross-linking of a Ser and a Cys-Ser pair usually separated by 7 or 8 residues along the peptide chain. The Ser residues are dehydrated to didehydroalanines, then bonded between their beta carbons. The alpha carbonyl of the Cys condenses with alpha carbon of the first Ser to form a pyridinyl ring. The ring may be mutiply dehydrogenated to form a pyridine ring with loss of the amino nitrogen of the first Ser. The amidation of Ser-17 probably does not occur by the same mechanism, oxidative cleavage of glycine, as in eukaryotes.
Source: (natural) STREPTOMYCES AZUREUS (bacteria) / References: UniProt: P0C8P8, THIOSTREPTON
#3: RNA chain RNA


Mass: 18693.145 Da / Num. of mol.: 1 / Fragment: RESIDUES 1051-1108 / Source method: isolated from a natural source / Source: (natural) THERMOTOGA MARITIMA (bacteria)
Compound detailsTHIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC ...THIOSTREPTON IS A MEMBER OF A SULPHUR-RICH HETEROCYCLIC PEPTIDES CLASS. ALL SHARE A MACROCYLIC CORE, CONSISTING OF A NITROGEN CONTAINING, SIX-MEMBERED RING CENTRAL TO DEHYDROAMINO ACIDS AND A SUBSET OF FIVE MEMBER RING STRUCTURES INCLUDING THIAZOLES, THIAZOLINES AND OXAZOLES. HERE, THIOSTREPTON IS REPRESENTED BY THE SEQUENCE (SEQRES) GROUP: 1 NAME: THIOSTREPTON CHAIN: B COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 0 TO 18 DESCRIPTION: THIOSTREPTON IS A HETEROCYCLIC THIOPEPTIDE, CONSISTING OF FOUR THIAZOLES ONE THIAZOLINE ONE PIPERIDEINE RINGS. A MODIFIED QUINOLINE LINKED TO MAIN-CHAIN RESIDUE 1 AND SIDE-CHAIN OF RESIDUE 12. THE OBSERVED C-TERMINAL AMINO GROUP NH2(18) IS LIKELY TO BE A POST-TRANSLATIONAL DECARBOXYLATED REMNANT OF A SER C-TERMINAL RESIDUE.

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Experimental details

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Experiment

Experiment
Method
SOLUTION NMR
THEORETICAL MODEL
NMR experimentType: NOESY
NMR detailsText: 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 conditionsIonic strength: 100 MM NACL, 5 MM MGCL2 / pH: 6.2 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Data collection

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR softwareName: rDOCK / Developer: DAVID MORLEY / Classification: refinement
RefinementMethod: 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 ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION AND BEST OVERALL DOCKING SCORE
Conformers submitted total number: 1

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