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- PDB-3iyr: tmRNA-SmpB: a journey to the center of the bacterial ribosome -

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Basic information

Entry
Database: PDB / ID: 3iyr
TitletmRNA-SmpB: a journey to the center of the bacterial ribosome
Components
  • SsrA-binding protein
  • tmRNA
KeywordsRIBOSOMAL PROTEIN/RNA / TMRNA / SMPB / RIBOSOME / TRANS-TRANSLATION / RIBOSOMAL PROTEIN-RNA complex
Function / homology
Function and homology information


trans-translation / rRNA binding / cytoplasm
Similarity search - Function
SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein.
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / SsrA-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13 Å
AuthorsWeis, F. / Bron, P. / Giudice, E. / Rolland, J.P. / Thomas, D. / Felden, B. / Gillet, R.
CitationJournal: EMBO J / Year: 2010
Title: tmRNA-SmpB: a journey to the centre of the bacterial ribosome.
Authors: Félix Weis / Patrick Bron / Emmanuel Giudice / Jean-Paul Rolland / Daniel Thomas / Brice Felden / Reynald Gillet /
Abstract: Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on ...Ribosomes mediate protein synthesis by decoding the information carried by messenger RNAs (mRNAs) and catalysing peptide bond formation between amino acids. When bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger RNA bound to small protein B (tmRNA-SmpB ribonucleoprotein complex). Trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. Here, we present the cryo-electron microscopy structures of tmRNA-SmpB accommodated or translocated into stalled ribosomes. Two atomic models for each state are proposed. This study reveals how tmRNA-SmpB crosses the ribosome and how, as the problematic mRNA is ejected, the tmRNA resume codon is placed onto the ribosomal decoding site by new contacts between SmpB and the nucleotides upstream of the tag-encoding sequence. This provides a structural basis for the transit of the large tmRNA-SmpB complex through the ribosome and for the means by which the tmRNA internal frame is set for translation to resume.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_imaging_optics / em_software
Item: _em_imaging_optics.energyfilter_name / _em_software.image_processing_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_ref_seq_dif.details

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: tmRNA
B: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)130,3022
Polymers130,3022
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain tmRNA


Mass: 112818.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: AP008226.1
#2: Protein SsrA-binding protein


Mass: 17483.176 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q8RR57

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Thermus thermophilus 70S ribosome / Type: RIBOSOME
Molecular weightValue: 2.3 MDa / Experimental value: NO
Buffer solutionpH: 7.5
Details: 5mM Hepes-KOH (pH 7.5), 10mM NH4Cl, 10mM MgOAc, 50mM KCl, 0.1mM EDTA and 6mM BetaME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 5mM Hepes-KOH (pH 7.5), 10mM NH4Cl, 10mM MgOAc, 50mM KCl, 0.1mM EDTA and 6mM BetaME
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 % / Method: Blot for 5 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL 2200FS / Date: Jul 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 45700 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm / Cs: 2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1MDFFmodel fitting
2UCSF Chimeramodel fitting
3IMAGIC53D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 13 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 70761 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteriaDetails
1FLEXIBLE FITREALCross-CorrelationREFINEMENT PROTOCOL--Rigid Body and flexible fitting DETAILS--The domains were initially separately fitted by manual docking and then further optimized using mdff. A model of SmpB C-terminal Tail (KAYEKRREDKKEAVRRALEEL) was added.
2FLEXIBLE FITREALCross-CorrelationREFINEMENT PROTOCOL--Rigid Body and flexible fitting DETAILS--each subdomain (H2b-c, H5, pk1, pk2, pk3, pk4) were initially separately fitted by manual docking and then further optimized using mdff.
Atomic model building

Pdb chain-ID: B / Source name: PDB / Type: experimental model

IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-ID
12CZJ

2czj

12CZJ1
22OB7

2ob7

22OB72
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1175 7466 0 0 8641

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