SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. Similarity search - Domain/homology
Journal: 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.
Energyfilter name: In-column Omega Filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
-
Processing
EM software
ID
Name
Version
Category
1
MDFF
modelfitting
2
UCSF Chimera
modelfitting
3
IMAGIC
5
3Dreconstruction
CTF correction
Details: Each particle
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 13 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 49061 / Symmetry type: POINT
Atomic model building
ID
Protocol
Space
Target criteria
Details
1
FLEXIBLEFIT
REAL
Cross-Correlation
REFINEMENT PROTOCOL--Rigid Body and flexible fitting DETAILS--The domains were initially separately fitted by manual docking and then further optimized using mdff.
2
FLEXIBLEFIT
REAL
Cross-Correlation
REFINEMENT 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
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