1C4L image
Deposition Date 1999-08-30
Release Date 2000-08-09
Last Version Date 2023-12-27
Entry Detail
PDB ID:
1C4L
Keywords:
RNA
Title:
SOLUTION STRUCTURE OF AN RNA DUPLEX INCLUDING A C-U BASE-PAIR
Biological Source:
Source Organism:
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
50
Conformers Submitted:
1
Selection Criteria:
SUMMATION OF TOTAL ENERGY (COVALENT GEOMETRY, NON-BOND ENERGY, DISTANCE AND DIHEDRAL ANGLE CONSTRAINTS)
1C4L validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*GP*AP*CP*UP*CP*AP*GP*G)-3')
Chain IDs:A
Chain Length:9
Number of Molecules:1
Biological Source:
Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(*CP*CP*UP*GP*CP*GP*UP*CP*G)-3')
Chain IDs:B
Chain Length:9
Number of Molecules:1
Biological Source:
Ligand Molecules
NA
Primary Citation
Solution structure of an RNA duplex including a C-U base pair.
Biochemistry 39 7074 7080 (2000)
PMID: 10852704 DOI: 10.1021/bi000018m

Abstact

The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
1C4L