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- EMDB-47655: Cryo-EM structure of RaiA RNA from Clostridium acetobutylicum -

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Basic information

Entry
Database: EMDB / ID: EMD-47655
TitleCryo-EM structure of RaiA RNA from Clostridium acetobutylicum
Map data
Sample
  • Complex: RaiA RNA from Clostridium acetobutylicum
    • RNA: RNA (204-MER)
KeywordsNon-coding RNA / cryo-EM / raiA motif RNA / KhpA / KhpB / ModT / RNA
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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)R35GM131901 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 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
DepositionOct 31, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47655.png

Downloads & links

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Map

FileDownload / File: emd_47655.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å		0.86 Å/pix.
x 256 pix.
= 219.136 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
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Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.08614437 - 0.2663464
Average (Standard dev.)0.00066404644 (±0.0065014944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.136 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47655_msk_1.map
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Half map: #2

Fileemd_47655_half_map_1.map
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Half map: #1

Fileemd_47655_half_map_2.map
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Sample components

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Entire : RaiA RNA from Clostridium acetobutylicum

EntireName: RaiA RNA from Clostridium acetobutylicum
Components
  • Complex: RaiA RNA from Clostridium acetobutylicum
    • RNA: RNA (204-MER)

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Supramolecule #1: RaiA RNA from Clostridium acetobutylicum

SupramoleculeName: RaiA RNA from Clostridium acetobutylicum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)

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Macromolecule #1: RNA (204-MER)

MacromoleculeName: RNA (204-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)
Molecular weightTheoretical: 66.104234 KDa
SequenceString: UUAAGUUAGG UUUGUGGUUG AAAGUCGAUG CCAGUCGCAG GCAAAACGAU CCACGUAAGU UAAACAAAGU UUUAAUGAGC AUGGUGCGG CUUAGAAGUA AGUCCUGCCG CUUUAGGCGA GAGUAUUAGU AGUGAGAGGG UAAUUCCGGG UAGCGAAACU U CCAGCAGG ...String:
UUAAGUUAGG UUUGUGGUUG AAAGUCGAUG CCAGUCGCAG GCAAAACGAU CCACGUAAGU UAAACAAAGU UUUAAUGAGC AUGGUGCGG CUUAGAAGUA AGUCCUGCCG CUUUAGGCGA GAGUAUUAGU AGUGAGAGGG UAAUUCCGGG UAGCGAAACU U CCAGCAGG CGAGUGUGGG GUCAAAGACC AGGUCAACUA ACUUAA

GENBANK: GENBANK: AE001437.1

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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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 439963
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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