During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (Psi) allows efficient recognition and readthrough of these stop codons by a transfer RNA(tRNA), although it requires the formation of two normally forbidden purine-purine base pairs(1). Here we determined the crystal structure at 3.1 angstrom resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the Psi AG stop codon in the A site. The Psi A base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs.