[English] 日本語
Yorodumi
- PDB-3iyq: tmRNA-SmpB: a journey to the center of the bacterial ribosome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3iyq
TitletmRNA-SmpB: a journey to the center of the bacterial ribosome
Components
  • SsrA-binding protein
  • tmRNATransfer-messenger RNA
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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-5188
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5188
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tmRNA
B: SsrA-binding protein


Theoretical massNumber of molelcules
Total (without water)130,3022
Polymers130,3022
Non-polymers00
Water0
1


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

-
Components

#1: RNA chain tmRNA / Transfer-messenger RNA


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

-
Experimental details

-
Experiment

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

-
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

-
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 FIELDBright-field microscopy / 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

-
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: 49061 / 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.
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
12CZJ12CZJ1
22OB722OB72
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms992 7466 0 0 8458

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more