3A3A

Crystal structure of human selenocystine tRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of human selenocysteine tRNA.

Itoh, Y.Chiba, S.Sekine, S.Yokoyama, S.

(2009) Nucleic Acids Res 37: 6259-6268

  • DOI: https://doi.org/10.1093/nar/gkp648
  • Primary Citation of Related Structures:  
    3A3A

  • PubMed Abstract: 

    Selenocysteine (Sec) is the 21st amino acid in translation. Sec tRNA (tRNA(Sec)) has an anticodon complementary to the UGA codon. We solved the crystal structure of human tRNA(Sec). tRNA(Sec) has a 9-bp acceptor stem and a 4-bp T stem, in contrast with the 7-bp acceptor stem and the 5-bp T stem in the canonical tRNAs. The acceptor stem is kinked between the U6:U67 and G7:C66 base pairs, leading to a bent acceptor-T stem helix. tRNA(Sec) has a 6-bp D stem and a 4-nt D loop. The long D stem includes unique A14:U21 and G15:C20a pairs. The D-loop:T-loop interactions include the base pairs G18:U55 and U16:U59, and a unique base triple, U20:G19:C56. The extra arm comprises of a 6-bp stem and a 4-nt loop. Remarkably, the D stem and the extra arm do not form tertiary interactions in tRNA(Sec). Instead, tRNA(Sec) has an open cavity, in place of the tertiary core of a canonical tRNA. The linker residues, A8 and U9, connecting the acceptor and D stems, are not involved in tertiary base pairing. Instead, U9 is stacked on the first base pair of the extra arm. These features might allow tRNA(Sec) to be the target of the Sec synthesis/incorporation machineries.


  • Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
selenocysteine tRNA90Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.949α = 90
b = 51.573β = 101.64
c = 81.365γ = 90
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Refinement description