1MVR

Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome

Summary for 1MVR

• Entry DOI: 10.2210/pdb1mvr/pdb
• Related: 1GIX 1GIY 1GQE 1MI6
• EMDB information: 1006 1007 1008 1009 1010
• Descriptor: mRNA, triplet codon (A-site), Helix 34 of 16S rRNA, Helix 44 of 16S rRNA, ... (8 entities in total)
• Functional Keywords: rf2, release complex, conformational changes, ribosome
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 110229.45

Authors

Rawat, U.B.,Zavialov, A.V.,Sengupta, J.,Valle, M.,Grassucci, R.A.,Linde, J.,Vestergaard, B.,Ehrenberg, M.,Frank, J. (deposition date: 2002-09-26, release date: 2003-04-01, Last modification date: 2024-02-14)

Primary citation

Rawat, U.B.,Zavialov, A.V.,Sengupta, J.,Valle, M.,Grassucci, R.A.,Linde, J.,Vestergaard, B.,Ehrenberg, M.,Frank, J.
A cryo-electron microscopic study of ribosome-bound termination factor RF2
Nature, 421:87-90, 2003

PubMed Abstract: Protein synthesis takes place on the ribosome, where genetic information carried by messenger RNA is translated into a sequence of amino acids. This process is terminated when a stop codon moves into the ribosomal decoding centre (DC) and is recognized by a class-1 release factor (RF). RFs have a conserved GGQ amino-acid motif, which is crucial for peptide release and is believed to interact directly with the peptidyl-transferase centre (PTC) of the 50S ribosomal subunit. Another conserved motif of RFs (SPF in RF2) has been proposed to interact directly with stop codons in the DC of the 30S subunit. The distance between the DC and PTC is approximately 73 A. However, in the X-ray structure of RF2, SPF and GGQ are only 23 A apart, indicating that they cannot be at DC and PTC simultaneously. Here we show that RF2 is in an open conformation when bound to the ribosome, allowing GGQ to reach the PTC while still allowing SPF-stop-codon interaction. The results indicate new interpretations of accuracy in termination, and have implications for how the presence of a stop codon in the DC is signalled to PTC.

PubMed: 12511960
DOI: 10.1038/nature01224

Experimental method

ELECTRON MICROSCOPY (12.8 Å)