1Q9A

Crystal structure of the sarcin/ricin domain from E.coli 23S rRNA at 1.04 resolution

Summary for 1Q9A

• Entry DOI: 10.2210/pdb1q9a/pdb
• Related: 1JBR 1JBS 1MSY 1Q93 1Q96 480D 483D
• Descriptor: Sarcin/ricin 23S rRNA (2 entities in total)
• Functional Keywords: sarcin/ricin domain, ribonucleic acid, rna recognition, high resolution, ribosomes, rna
• Total number of polymer chains: 1
• Total formula weight: 8744.25

Authors

Correll, C.C.,Beneken, J.,Plantinga, M.J.,Lubbers, M.,Chan, Y.L. (deposition date: 2003-08-22, release date: 2003-11-25, Last modification date: 2024-02-14)

Primary citation

Correll, C.C.,Beneken, J.,Plantinga, M.J.,Lubbers, M.,Chan, Y.L.
The common and distinctive features of the bulged-G motif based on a 1.04 A resolution RNA structure
Nucleic Acids Res., 31:6806-6818, 2003

PubMed Abstract: Bulged-G motifs are ubiquitous internal RNA loops that provide specific recognition sites for proteins and RNAs. To establish the common and distinctive features of the motif we determined the structures of three variants and compared them with related structures. The variants are 27-nt mimics of the sarcin/ricin loop (SRL) from Escherichia coli 23S ribosomal RNA that is an essential part of the binding site for elongation factors (EFs). The wild-type SRL has now been determined at 1.04 A resolution, supplementing data obtained before at 1.11 A and allowing the first calculation of coordinate error for an RNA motif. The other two structures, having a viable (C2658U*G2663A) or a lethal mutation (C2658G*G2663C), were determined at 1.75 and 2.25 A resolution, respectively. Comparisons reveal that bulged-G motifs have a common hydration and geometry, with flexible junctions at flanking structural elements. Six conserved nucleotides preserve the fold of the motif; the remaining seven to nine vary in sequence and alter contacts in both grooves. Differences between accessible functional groups of the lethal mutation and those of the viable mutation and wild-type SRL may account for the impaired elongation factor binding to ribosomes with the C2658G*G2663C mutation and may underlie the lethal phenotype.

PubMed: 14627814
DOI: 10.1093/nar/gkg908

Experimental method

X-RAY DIFFRACTION (1.04 Å)