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Related Experiment Video

Updated: Mar 10, 2026

Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

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Published on: January 9, 2015

Cryo-EM structures reveal a conserved architecture for raiA noncoding RNA.

Yao He^1,2, Janet Zhong¹, Yuan Yang¹

¹Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095-1569, United States.

Nucleic Acids Research

|March 9, 2026

Summary

RaiA motif RNA, abundant in bacteria, has an unknown function. Cryo-EM structures reveal a conserved core architecture, suggesting a crucial role for the P1 stem in this noncoding RNA family.

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Do's and Don'ts of Cryo-electron Microscopy: A Primer on Sample Preparation and High Quality Data Collection for Macromolecular 3D Reconstruction

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Area of Science:

Structural biology
Microbiology
RNA biology

Background:

RaiA motif RNA is a widespread bacterial noncoding RNA (ncRNA) family.
Its cellular abundance and knockout phenotypes suggest importance, but its function is unknown.

Purpose of the Study:

To determine the high-resolution structures of RaiA motif RNAs from different bacterial species.
To elucidate the conserved structural framework of RaiA motif RNAs.

Main Methods:

Cryogenic electron microscopy (cryo-EM) was used to determine structures.
Structures were solved for three RaiA motif RNAs and a minimal variant.

Main Results:

Cryo-EM structures revealed a conserved core architecture with conserved tertiary interactions in pseudoknots PK1 and PK2.
Peripheral stems varied, but the P1 stem was remarkably conserved in length, structure, and interactions.
A minimal 113-nucleotide variant was also structurally characterized.

Conclusions:

The study defines the conserved structural framework of RaiA motif RNAs.
The conserved P1 stem suggests a critical, essential role.
This work provides a foundation for future structure-based functional studies of RaiA motif RNAs and highlights cryo-EM's utility for ncRNA structure determination.