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PDBsum entry 3f1f

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Ribosome PDB id
3f1f
Jmol
Contents
Protein chains
271 a.a.
204 a.a.
202 a.a.
181 a.a.
159 a.a.
145 a.a.
147 a.a.
137 a.a.
122 a.a.
146 a.a.
134 a.a.
117 a.a.
98 a.a.
137 a.a.
117 a.a.
101 a.a.
112 a.a.
92 a.a.
100 a.a.
187 a.a.
76 a.a.
88 a.a.
62 a.a.
59 a.a.
30 a.a.
52 a.a.
44 a.a.
48 a.a.
63 a.a.
DNA/RNA
Metals
_MG ×1060

References listed in PDB file
Key reference
Title Crystal structure of a translation termination complex formed with release factor rf2.
Authors A.Korostelev, H.Asahara, L.Lancaster, M.Laurberg, A.Hirschi, J.Zhu, S.Trakhanov, W.G.Scott, H.F.Noller.
Ref. Proc Natl Acad Sci U S A, 2008, 105, 19684-19689. [DOI no: 10.1073/pnas.0810953105]
PubMed id 19064930
Abstract
We report the crystal structure of a translation termination complex formed by the Thermus thermophilus 70S ribosome bound with release factor RF2, in response to a UAA stop codon, solved at 3 A resolution. The backbone of helix alpha5 and the side chain of serine of the conserved SPF motif of RF2 recognize U1 and A2 of the stop codon, respectively. A3 is unstacked from the first 2 bases, contacting Thr-216 and Val-203 of RF2 and stacking on G530 of 16S rRNA. The structure of the RF2 complex supports our previous proposal that conformational changes in the ribosome in response to recognition of the stop codon stabilize rearrangement of the switch loop of the release factor, resulting in docking of the universally conserved GGQ motif in the PTC of the 50S subunit. As seen for the RF1 complex, the main-chain amide nitrogen of glutamine in the GGQ motif is positioned to contribute directly to catalysis of peptidyl-tRNA hydrolysis, consistent with mutational studies, which show that most side-chain substitutions of the conserved glutamine have little effect. We show that when the H-bonding capability of the main-chain N-H of the conserved glutamine is eliminated by substitution with proline, peptidyl-tRNA esterase activity is abolished, consistent with its proposed role in catalysis.
Figure 1.
Comparison of the structures of the RF1 and RF2 termination complexes. (A) RF2 termination complex (this work), showing RF2 (yellow), P-site tRNA (orange), E-site tRNA (red), mRNA (green), 16S rRNA (cyan), 23S and 5S rRNA (gray), 30S proteins (blue), and 50S proteins (magenta). (B) RF1 termination complex (9); molecular components are colored similarly as in A. (C) RF2 in its ribosome-bound conformation, rotated ≈180° from the view shown in A, with domains numbered. The GGQ and SPF motifs are shown in red, and the switch loop is shown in orange. (D) RF1 in its ribosome-bound conformation. The GGQ and PVT motifs are indicated in red and the switch loop is shown in orange.
Figure 2.
Interactions with the UAA stop codon in the decoding center in the RF1 and RF2 termination complexes. (A) Stereoview of the σ[A]-weighted 3F[obs] − 2F[calc] electron density map of the stop codon and surrounding elements of RF2 and the ribosome. Electron density is contoured at 1.0 σ for RF2, and at 1.5 σ for rRNA and mRNA, and colored yellow (RF1), green (mRNA), and blue (16S rRNA). (B) Interaction of the hydroxyl group of Ser-206 of the SPF motif of RF2 with A2 of the stop codon. (C) Interaction of Thr-216 of RF2 with A3 of the stop codon. (D) Comparison of the positions of Thr-186 of the PVT motif of RF1 (gray) and Ser-206 of the SPF motif of RF2 (yellow), showing their different modes of recognition of U1 and A2 of the UAA stop codon. The structures of the two termination complexes were globally superimposed. (E) Packing of RF2 around A3 of the UAA stop codon. Val-203 would be positioned to exclude water from H-bonding to O6 of guanine, helping to discriminate against guanine at position 3. The structure model is represented as Van der Waals surfaces for RF2 (yellow) and mRNA (green); 16S rRNA is shown in blue.
PROCHECK
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