Conformational changes in release factors and the ribosomal decoding centre. Release factor conformations are shown in (A) absence of the ribosome (from PDB entry 2IHR ), (B) bound to the ribosome containing a UAA stop codon (from PDB entry 3D5A ). The catalytic domain 3 is indicated in blue, the stop codon recognition domain (consisting of domains 2 and 4) is shown in orange and domain 1 is colored red. The switch loop is highlighted in green. The conformation of the universally conserved ribosome decoding site nucleotides A-1492 and A-1493 is shown (C) in case of an empty A-site with both bases stacked (from PDB entry 1J5E ), (D) with mRNA and a cognate tRNA present in the A-site and both bases unstacked (from PDB entry 1IBM ) and (E) with a stop codon and a release factor present in the A-site in an intermediate state (from PDB entry 3MR8 ). The mRNA present in the A-site is shown in green in panel D (UUU) and panel E (UAA), the conserved decoding centre in cyan. The tRNA molecule (panel D) and release factor molecule (panel E) have been omitted for clarity.