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Mapping of SmpB-footprinted nucleotides on the 3D structure of the ribosome

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posted on 2011-12-31, 00:05 authored by Natalia Ivanova, Michael Y. Pavlov, Elli Bouakaz, Måns Ehrenberg, Lovisa Holmberg Schiavone

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Taken from "Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA"

Nucleic Acids Research 2005;33(11):3529-3539.

Published online 21 Jun 2005


© The Author 2005. Published by Oxford University Press. All rights reserved

() Nucleotides in 16S rRNA protected by SmpB bound to the free 30S subunit (painted blue, purple and red) and to the 70S ribosome (red). () Nucleotides in 23S rRNA protected by SmpB in the free 50S subunit (green and orange) and in the 70S ribosome (green) shown together with the positions of 16S rRNA protected in the 70S ribosome (red). The A-site (A and B) and P-site (B) tRNAs are painted in yellow and the A-, P- and E-sites are indicated. Both subunits are shown from the interface side. The location of the head, body, neck and platform are indicated on the 30S subunit (A) and the location of the L1 and L7/L12 stalks are indicated on the 50S subunit (B). The 3D structures of the 16S rRNA and 23S rRNA are from the 1PNS and 1PNU PDB files. Nucleotide positions are given in sequence numbering, which differs from that used in the 1PNS and 1PNU PDB files.


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