PDBsum entry 2qa4

Ribosome

PDB id: 2qa4

Contents

Protein chains

237 a.a.

337 a.a.

246 a.a.

140 a.a.

172 a.a.

119 a.a.

125 a.a.

160 a.a.

118 a.a.

142 a.a.

132 a.a.

145 a.a.

194 a.a.

186 a.a.

115 a.a.

143 a.a.

95 a.a.

150 a.a.

81 a.a.

119 a.a.

53 a.a.

65 a.a.

154 a.a.

82 a.a.

142 a.a.

73 a.a.

56 a.a.

46 a.a.

92 a.a.

DNA/RNA

Metals

_CL ×22

_NA ×86

_MG ×116

_CD ×5

__K ×2

References listed in PDB file

Key reference

Title

Structure of the base of the l7/l12 stalk of the haloarcula marismortui large ribosomal subunit: analysis of l11 movements.

Authors

J.M.Kavran, T.A.Steitz.

Ref.

J Mol Biol, 2007, 371, 1047-1059. [DOI no: 10.1016/j.jmb.2007.05.091]

PubMed id

17599351

Abstract

Initiation factors, elongation factors, and release factors all interact with the L7/L12 stalk of the large ribosomal subunit during their respective GTP-dependent cycles on the ribosome. Electron density corresponding to the stalk is not present in previous crystal structures of either 50 S subunits or 70 S ribosomes. We have now discovered conditions that result in a more ordered factor-binding center in the Haloarcula marismortui (H.ma) large ribosomal subunit crystals and consequently allows the visualization of the full-length L11, the N-terminal domain (NTD) of L10 and helices 43 and 44 of 23 S rRNA. The resulting model is currently the most complete reported structure of a L7/L12 stalk in the context of a ribosome. This region contains a series of intermolecular interfaces that are smaller than those typically seen in other ribonucleoprotein interactions within the 50 S subunit. Comparisons of the L11 NTD position between the current structure, which is has an NTD splayed out with respect to previous structures, and other structures of ribosomes in different functional states demonstrates a dynamic range of L11 NTD movements. We propose that the L11 NTD moves through three different relative positions during the translational cycle: apo-ribosome, factor-bound pre-GTP hydrolysis and post-GTP hydrolysis. These positions outline a pathway for L11 NTD movements that are dependent on the specific nucleotide state of the bound ligand. These three states are represented by the orientations of the L11 NTD relative to the ribosome and suggest that L11 may play a more specialized role in the factor binding cycle than previously appreciated.

Figure 2.
Figure 2. Interfaces between stalk components of the large ribosomal subunit. (a) A bifurcated stalk is formed on H43/44 RNA (red, space fill) with one lobe formed by L10 (green, ribbons) and one lobe formed by L11 (yellow, ribbons). The L11 NTD is extending away from the ribosome. (b) The N-terminal extension of L10 recognizes A1150 of 23 S RNA through interactions with Ile12 and Arg69. (c) The interactions between L10 and L11 are minimal and stabilized by each proteins respective interactions with the stalk RNA.

Figure 3.
Figure 3. Unassigned electron density with alpha-helical proportions. A stereo image of a difference Fourier map calculated between 50–4 Å resolution and contoured at 2 σ using F[o] amplitudes from NAC soaked ribosome crystals and F[c] amplitudes calculated from the model containing the newly built base of the stalk. The unassigned density (orange) has α-helical proportions and occupies a position near the C terminus of L10 NTD (green, ribbons).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 1047-1059) copyright 2007.