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- EMDB-72663: Cryo-EM structure of raiA motif RNA from Thermosediminibacter oceani -

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Basic information

Entry
Database: EMDB / ID: EMD-72663
TitleCryo-EM structure of raiA motif RNA from Thermosediminibacter oceani
Map data
Sample
  • Complex: raiA motif RNA from Thermosediminibacter oceani
KeywordsNon-coding RNA / cryo-EM / raiA motif RNA / KhpA / KhpB / ModT / RNA
Biological speciesThermosediminibacter oceani DSM 16646 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.7 Å
AuthorsHe Y / Zhong J / Yang Y / Gunsalus RP / Zhou ZH / Feigon J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM131901 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM071940 United States
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Cryo-EM structures reveal a conserved architecture for raiA noncoding RNA.
Authors: Yao He / Janet Zhong / Yuan Yang / Robert P Gunsalus / Z Hong Zhou / Juli Feigon /
Abstract: RaiA motif RNA is a family of bacterial noncoding RNAs (ncRNAs) found in over 2700 bacterial species. Although its cellular abundance is comparable to that of rRNAs and tRNAs in the human ...RaiA motif RNA is a family of bacterial noncoding RNAs (ncRNAs) found in over 2700 bacterial species. Although its cellular abundance is comparable to that of rRNAs and tRNAs in the human pathogen Clostridioides difficile and its knockout results in pronounced phenotypes, its function remains unknown. Sequence conservation analysis predicted a consensus secondary structure of raiA motif RNA with several major subtypes that differ in the number and composition of stems. Here, we present cryogenic electron microscopy (cryo-EM) structures of three raiA motif RNAs from three bacterial species, one from each subtype, at 3.0-3.5 Å resolution, as well as a minimal variant with 113 nucleotides at ∼8 Å resolution. Comparison of the structures reveals a conserved architecture, with a compact core comprising stems P3a-P3b bent by an asymmetric internal loop, P4, pseudoknot 1 (PK1), and PK2 with unusual tertiary interactions. While most of the peripheral stems vary, the length, structure, and tertiary interactions of the closing P1 are remarkably conserved, suggesting an essential role. Our study defines the conserved structural framework of raiA motif RNAs and provides a foundation for structure-based functional studies. This work also highlights the utility of cryo-EM for de novo structure determination of ncRNAs.
History
DepositionSep 11, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72663.png

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Map

FileDownload / File: emd_72663.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 128 pix.
= 219.136 Å		1.71 Å/pix.
x 128 pix.
= 219.136 Å		1.71 Å/pix.
x 128 pix.
= 219.136 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.712 Å
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Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.26038468 - 0.81876445
Average (Standard dev.)0.001961803 (±0.02552631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 219.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72663_msk_1.map
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Half map: #1

Fileemd_72663_half_map_1.map
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Half map: #2

Fileemd_72663_half_map_2.map
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Sample components

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Entire : raiA motif RNA from Thermosediminibacter oceani

EntireName: raiA motif RNA from Thermosediminibacter oceani
Components
  • Complex: raiA motif RNA from Thermosediminibacter oceani

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Supramolecule #1: raiA motif RNA from Thermosediminibacter oceani

SupramoleculeName: raiA motif RNA from Thermosediminibacter oceani / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermosediminibacter oceani DSM 16646 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 189412
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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