2CZJ

Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.

Bessho, Y.Shibata, R.Sekine, S.Murayama, K.Higashijima, K.Hori-Takemoto, C.Shirouzu, M.Kuramitsu, S.Yokoyama, S.

(2007) Proc.Natl.Acad.Sci.Usa 104: 8293-8298

  • DOI: 10.1073/pnas.0700402104
  • Primary Citation of Related Structures:  1WJX

  • PubMed Abstract: 
  • tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the tmRNA from Thermus thermophilus. Overall, the ribonucl ...

    tmRNA and small protein B (SmpB) are essential trans-translation system components. In the present study, we determined the crystal structure of SmpB in complex with the entire tRNA domain of the tmRNA from Thermus thermophilus. Overall, the ribonucleoprotein complex (tRNP) mimics a long-variable-arm tRNA (class II tRNA) in the canonical L-shaped tertiary structure. The tmRNA terminus corresponds to the acceptor and T arms, or the upper part, of tRNA. On the other hand, the SmpB protein simulates the lower part, the anticodon and D stems, of tRNA. Intriguingly, several amino acid residues collaborate with tmRNA bases to reproduce the canonical tRNA core layers. The linker helix of tmRNA had been considered to correspond to the anticodon stem, but the complex structure unambiguously shows that it corresponds to the tRNA variable arm. The tmRNA linker helix, as well as the long variable arm of class II tRNA, may occupy the gap between the large and small ribosomal subunits. This suggested how the tRNA domain is connected to the mRNA domain entering the mRNA channel. A loop of SmpB in the tRNP is likely to participate in the interaction with alanyl-tRNA synthetase, which may be the mechanism for the promotion of tmRNA alanylation by the SmpB protein. Therefore, the tRNP may simulate a tRNA, both structurally and functionally, with respect to aminoacylation and ribosome entry.


    Organizational Affiliation

    Genomic Sciences Center, Yokohama Institute, RIKEN 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SsrA-binding protein
A, C, E, G
123Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: smpB
Find proteins for Q8RR57 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RR57
Entity ID: 2
MoleculeChainsLengthOrganism
tmRNA (63-MER)B,D,F,H63N/A
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
B, D, F, H
RNA LINKINGC9 H13 N2 O9 PU
5MU
Query on 5MU
B, D, F, H
RNA LINKINGC10 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.776α = 90.00
b = 67.957β = 90.07
c = 178.662γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance