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- PDB-2jq7: Model for thiostrepton binding to the ribosomal L11-RNA -

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Basic information

Entry
Database: PDB / ID: 2jq7
TitleModel for thiostrepton binding to the ribosomal L11-RNA
Components
  • 50S RIBOSOMAL PROTEIN L11
  • RIBOSOMAL RNA
  • THIOSTREPTON
KeywordsRIBOSOME/ANTIBIOTIC / RIBOSOME-ANTIBIOTIC COMPLEX / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / THIAZOLINE / 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, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / 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 ...Thiazolylpeptide-type bacteriocin precursor / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L11/L12, C-terminal domain / 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 / Arc Repressor Mutant, subunit A / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
THIOSTREPTON / RNA / RNA (> 10) / Thiostrepton / Large ribosomal subunit protein uL11
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
STREPTOMYCES AZUREUS (bacteria)
Escherichia coli (E. coli)
MethodSOLUTION NMR / DOCKING
AuthorsJonker, H.R.A. / Ilin, S. / Grimm, S.K. / Woehnert, J. / Schwalbe, H.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: L11 Domain Rearrangement Upon Binding to RNA and Thiostrepton Studied by NMR Spectroscopy
Authors: Jonker, H.R.A. / Ilin, S. / Grimm, S.K. / Woehnert, J. / Schwalbe, H.
History
DepositionMay 30, 2007Deposition site: BMRB / Processing site: RCSB
SupersessionJul 3, 2007ID: 2NYO
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5May 27, 2015Group: Source and taxonomy
Revision 1.6Nov 1, 2017Group: Derived calculations / Structure summary / Category: pdbx_nmr_representative / pdbx_struct_assembly
Item: _pdbx_nmr_representative.selection_criteria / _pdbx_struct_assembly.method_details
Revision 2.0Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Polymer sequence
Category: database_2 / entity_poly ...database_2 / entity_poly / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_nmr_exptl_sample.isotopic_labeling / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,6113
Polymers35,6113
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-37 kcal/mol
Surface area14870 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200TOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA
RepresentativeModel #1lowest energy

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Components

#1: Protein 50S RIBOSOMAL PROTEIN L11


Mass: 15111.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Gene: RPLK / Plasmid: PET11A / Production host: ESCHERICHIA COLI BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P29395
#2: RNA chain RIBOSOMAL RNA


Mass: 18693.145 Da / Num. of mol.: 1 / Fragment: L11 BINDING DOMAIN, RESIDUES 1051-1108 / Source method: obtained synthetically / Details: IN VITRO TRANSCRIBED RNA CONSTRUCT. / Source: (synth.) Escherichia coli (E. coli)
#3: Protein/peptide THIOSTREPTON


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
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)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: IPAP(1H, 15N)HSQC
NMR detailsText: THE RDC DATA WAS USED TO DETERMINE THE RELATIVE DOMAIN ORIENTATION OF THE L11 PROTEIN

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Sample preparation

DetailsType: solution
Contents: 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O
Label: sample_1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMRibosomal Protein L11[U-13C; U-15N; U-2H]1
0.3 mMRibosomal RNAnatural abundance1
0.3 mMThiostrepton Antibioticnatural abundance1
20 mMpotassium phosphatenatural abundance1
200 mMpotassium chloridenatural abundance1
Sample conditionsIonic strength: 220 / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2.0_DEVELDOMINGUEZ ET AL.refinement
TopSpin1.3Bruker Biospincollection
XwinNMR3.5Bruker Biospincollection
NMRPipe2.5Delaglio et al.processing
Sparky3.112Goddard et al.data analysis
CNS1.1Brunger et al.structure solution
RefinementMethod: DOCKING / Software ordinal: 1
Details: FOR CHAIN A, THE INITIAL COORDINATES ARE OPTIMIZED USING RDCS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE ...Details: FOR CHAIN A, THE INITIAL COORDINATES ARE OPTIMIZED USING RDCS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN C, THE INITIAL COORDINATES ARE FROM PDB ENTRY 1E9W. LEFT FLEXIBLE ACIDS AND NUCLEIC ACIDS WHICH DO NOT COMPLY WELL WITH THE ANTIBIOTIC IN THE CASE HERE.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: TOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA
Conformers calculated total number: 200 / Conformers submitted total number: 10

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