PDBsum entry 1dk1

Ribosome

PDB id: 1dk1

Contents

Protein chain

86 a.a. *

DNA/RNA

Metals

_NA ×2

__K

_MG ×9

Waters ×25

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the s15-Rrna complex.

Authors

A.Nikulin, A.Serganov, E.Ennifar, S.Tishchenko, N.Nevskaya, W.Shepard, C.Portier, M.Garber, B.Ehresmann, C.Ehresmann, S.Nikonov, P.Dumas.

Ref.

Nat Struct Biol, 2000, 7, 273-277. [DOI no: 10.1038/74028]

PubMed id

10742169

Abstract

In bacterial ribosomes, the small (30S) ribosomal subunit is composed of 16S rRNA and 21 distinct proteins. Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. Here we report the 2.8 ¿ resolution crystal structure of the highly conserved S15-rRNA complex. Protein S15 interacts in the minor groove with a G-U/G-C motif and a three-way junction. The latter is constrained by a conserved base triple and stacking interactions, and locked into place by magnesium ions and protein side chains, mainly through interactions with the unique three-dimensional geometry of the backbone. The present structure gives insights into the dual role of S15 in ribosome assembly and translational regulation.

Figure 1.
Figure 1. Components of the S15−rRNA complex. a, Sequence of the Thermus thermophilus S15 protein^17. Colored residues are >80% conserved among 23 bacterial sequences (green) and additionally conserved among 55 homologous sequences from plastids, Archaea and Eukarya (red). Amino acids that interact with the rRNA fragment are underlined, and the four -helices deduced from the crystallographic structure are indicated. b, Schematic of tertiary structure of the 57 nt RNA corresponding to nucleotides 584−590/649−667/739−757 of E. coli rRNA as determined by comparative sequence analysis, and contacts with protein. Nucleotides within the UUCG loops capping helices 21 and 22 are in italics. Bases in red are >95% conserved in 6,000 prokaryotic sequences. Ribose rings in black are in a C2'-endo conformation, stacking is shown by hatched lines, and water molecules are indicated by W. Two alternative conformations of G664 are shown. Nucleotide C748 is not well defined. Conserved amino acid residues are colored as in (a), and their contacts with RNA backbone (phosphate group or 2'-OH) or functional groups of bases are indicated. Contacts are with amino acid side chains, with the single exception of Gly 22, which interacts through the backbone carbonyl.

Figure 4.
Figure 4. Schematic representation of the recognition by S15 on rRNA, possible implications in 30S assembly and comparison with mRNA binding. S15 is schematized in green with its two RNA binding sites numbered 1 and 2. The first one recognizes a particular backbone geometry (the three-way junction in rRNA and the pseudoknot fold in mRNA). The second one recognizes an analogous G-U/G-C motif in both RNAs. In 16S rRNA, binding induces a conformational adjustment (widening of the deep groove), denoted by a red star, that is most likely required for subsequent 30S assembly steps (for example, S18 binding).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 273-277) copyright 2000.