2N2P image
Entry Detail
PDB ID:
2N2P
Keywords:
RNA
Title:
Solution structure of a double base-pair inversion mutant of murine tumour necrosis factor alpha CDE-23 RNA
Biological Source:
Source Organism:
synthetic construct
PDB Version:
Deposition Date:
2015-05-11
Release Date:
2015-08-05
Method Details:
Experimental Method:
SOLUTION NMR
Conformers Calculated:
100
Conformers Submitted:
10
Selection Criteria:
structures with the lowest energy
2N2P validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*GP*CP*AP*UP*GP*UP*UP*UP*AP*GP*UP*GP*UP*CP*UP*AP*AP*AP*CP*GP*GP*UP*U)-3')
Chain IDs:A
Chain Length:23
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
NA
Primary Citation
A Distinct, Sequence-Induced Conformation Is Required for Recognition of the Constitutive Decay Element RNA by Roquin.
Structure 23 1437 1447 (2015)
PMID: 26165594 DOI: 10.1016/j.str.2015.06.001

Abstact

The constitutive decay element (CDE) of tumor necrosis factor α (TNF-α) mRNA (Tnf) represents the prototype of a class of RNA motifs that mediate rapid degradation of mRNAs encoding regulators of the immune response and development. CDE-type RNAs are hairpin structures featuring a tri-nucleotide loop. The protein Roquin recognizes CDE-type stem loops and recruits the Ccr4-Caf1-Not deadenylase complex to the mRNA, thereby inducing its decay. Stem recognition does not involve nucleotide bases; however, there is a strong stem sequence requirement for functional CDEs. Here, we present the solution structures of the natural Tnf CDE and of a CDE mutant with impaired Roquin binding. We find that the two CDEs adopt unique and distinct structures in both the loop and the stem, which explains the ability of Roquin to recognize stem loops in a sequence-specific manner. Our findings result in a relaxed consensus motif for prediction of new CDE stem loops.

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Primary Citation of related structures
2N2O