357D image
Deposition Date 1997-10-09
Release Date 1997-12-01
Last Version Date 2024-02-21
Entry Detail
PDB ID:
357D
Keywords:
RNA
Title:
3.5 A structure of fragment I from E. coli 5S RRNA
Biological Source:
Source Organism(s):
Escherichia coli (Taxon ID: 562)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.50 Å
R-Value Free:
0.26
R-Value Work:
0.31
R-Value Observed:
0.31
Space Group:
P 61 2 2
357D validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA-DNA (5'-R(*UP*GP*DCP)-D(*CP(S)*)-R(*UP*GP*GP*CP*GP*GP*C)-3')
Chain IDs:A
Chain Length:11
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*CP*GP*AP*UP*GP*GP*UP*AP*GP*UP*GP*UP*GP*GP*GP*G*UP*C)-3')
Chain IDs:B
Chain Length:19
Number of Molecules:1
Biological Source:Escherichia coli
Polymer Type:polyribonucleotide
Molecule: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')
Chain IDs:C
Chain Length:31
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
SSU A U URIDINE-5'-PHOSPHOROTHIOATE
Ligand Molecules
HG
MG
Primary Citation
Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain.
Cell(Cambridge,Mass.) 91 705 712 (1997)
PMID: 9393863 DOI: 10.1016/S0092-8674(00)80457-2

Abstact

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.

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Primary Citation of related structures
357D
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