364D image
Deposition Date 1997-12-08
Release Date 1998-01-02
Last Version Date 2024-02-21
Entry Detail
PDB ID:
364D
Keywords:
RNA
Title:
3.0 A STRUCTURE OF FRAGMENT I FROM E. COLI 5S RRNA
Biological Source:
Source Organism:
Escherichia coli (Taxon ID: 562)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.00 Å
R-Value Free:
0.32
R-Value Work:
0.27
R-Value Observed:
0.27
Space Group:
P 61 2 2
364D validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*UP*GP*)-D(*(1SC)P*)-R(*CP*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
1SC A C 5'-O-THIOPHOSPHONOCYTIDINE
Ligand Molecules
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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Disease

Primary Citation of related structures
364D
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