357D

3.5 A structure of fragment I from E. coli 5S RRNA

Summary for 357D

• Entry DOI: 10.2210/pdb357d/pdb
• Descriptor: RNA-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3'), RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G*UP*C)-3'), RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*UP*AP*GP*G P*GP*AP*AP*CP*UP* GP*CP*CP*AP*GP*GP*CP*AP*U)-3'), ... (5 entities in total)
• Functional Keywords: u-rna, double helix, kinked, internal loop, overhanging base, modified, mismatched, rna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 3
• Total formula weight: 20087.96

Authors

Correll, C.C.,Freeborn, B.,Moore, P.B.,Steitz, T.A. (deposition date: 1997-10-09, release date: 1997-12-01, Last modification date: 2024-02-21)

Primary citation

Correll, C.C.,Freeborn, B.,Moore, P.B.,Steitz, T.A.
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
Cell(Cambridge,Mass.), 91:705-712, 1997

PubMed Abstract: Two new RNA structures portray how non-Watson-Crick base pairs and metal ions can produce a unique RNA shape suitable for recognition by proteins. The crystal structures of a 62 nt domain of E. coli 5S ribosomal RNA and a duplex dodecamer encompassing an internal loop E have been determined at 3.0 and 1.5 A, respectively. This loop E region is distorted by three "cross-strand purine stacks" and three novel, water-mediated noncanonical base pairs and stabilized by a four metal ion zipper. These features give its minor groove a unique hydrogen-bonding surface and make the adjacent major groove wide enough to permit recognition by the ribosomal protein L25, which is expected to bind to this surface.

PubMed: 9393863
DOI: 10.1016/S0092-8674(00)80457-2

Experimental method

X-RAY DIFFRACTION (3.5 Å)