spacer
spacer

PDBsum entry 3a3a
Go to PDB code: 
dna_rna links
RNA PDB id
3a3a

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
DNA/RNA
PDB id:
3a3a
Name: RNA
Title: Crystal structure of human selenocystine tRNA
Structure: Selenocysteine tRNA. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cell-free synthesis. Other_details: RNA was prepared by in vitro transcription with t7 RNA polymerase.
Resolution:
3.10Å     R-factor:   0.254     R-free:   0.314
Authors: Y.Itoh,S.Chiba,S.I.Sekine,S.Yokoyama
Key ref: Y.Itoh et al. (2009). Crystal structure of human selenocysteine tRNA. Nucleic Acids Res, 37, 6259-6268. PubMed id: 19692584
Date:
11-Jun-09     Release date:   11-Aug-09    
 Headers
 References

DNA/RNA chain
  G-C-C-C-G-G-A-U-G-A-U-C-C-U-C-A-G-U-G-G-U-C-U-G-G-G-G-U-G-C-A-G-G-C-U-U-C-A-A- 86 bases

 

 
Nucleic Acids Res 37:6259-6268 (2009)
PubMed id: 19692584  
 
 
Crystal structure of human selenocysteine tRNA.
Y.Itoh, S.Chiba, S.Sekine, S.Yokoyama.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20870747 R.L.Sherrer, Y.Araiso, C.Aldag, R.Ishitani, J.M.Ho, D.Söll, and O.Nureki (2011).
C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNA(Sec).
  Nucleic Acids Res, 39, 1034-1041.
PDB code: 3am1
  20446809 A.V.Lobanov, A.A.Turanov, D.L.Hatfield, and V.N.Gladyshev (2010).
Dual functions of codons in the genetic code.
  Crit Rev Biochem Mol Biol, 45, 257-265.  
19903474 J.Yuan, P.O'Donoghue, A.Ambrogelly, S.Gundllapalli, R.L.Sherrer, S.Palioura, M.Simonović, and D.Söll (2010).
Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems.
  FEBS Lett, 584, 342-349.  
  20847933 M.Rother, and J.A.Krzycki (2010).
Selenocysteine, pyrrolysine, and the unique energy metabolism of methanogenic archaea.
  Archaea, 2010, 0.  
20623998 S.Palioura, J.Herkel, M.Simonović, A.W.Lohse, and D.Söll (2010).
Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.
  Biol Chem, 391, 771-776.  
20306235 W.C.Hawkes, and Z.Alkan (2010).
Regulation of redox signaling by selenoproteins.
  Biol Trace Elem Res, 134, 235-251.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

spacer
spacer