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 1.3 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 U S A 104: 8293-8298

  • DOI: https://doi.org/10.1073/pnas.0700402104
  • Primary Citation of Related Structures:  
    1WJX, 2CZJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SsrA-binding proteinA,
B [auth C],
C [auth E],
D [auth G]
123Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q8RR57 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RR57 
Go to UniProtKB:  Q8RR57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RR57
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
tmRNA (63-MER)E [auth B],
F [auth D],
G [auth F],
H
63N/A
Sequence Annotations
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  • Reference Sequence
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
b = 67.957β = 90.07
c = 178.662γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description