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- EMDB-49873: ROOLfirm-tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-49873
TitleROOLfirm-tetramer
Map data
Sample
  • Organelle or cellular component: ROOLfirm-tetramer
    • RNA: ROOLefa-tetramer
Keywordsnatural RNA nanocage / drug delivery / RNA
Biological speciesFirmicutes bacterium CAG:227 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsLing XB / Fang WW / Ma JB / Korostelev AA
Funding support China, United States, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)NSFC 31971130 China
National Natural Science Foundation of China (NSFC)32471347 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM127094 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150953 United States
CitationJournal: Nature / Year: 2025
Title: Cryo-EM structure of a natural RNA nanocage.
Authors: Xiaobin Ling / Dmitrij Golovenko / Jianhua Gan / Jinbiao Ma / Andrei A Korostelev / Wenwen Fang /
Abstract: Long (>200 nucleotides) non-coding RNAs (lncRNAs) play important roles in diverse aspects of life. Over 20 classes of lncRNAs have been identified in bacteria and bacteriophages through comparative ...Long (>200 nucleotides) non-coding RNAs (lncRNAs) play important roles in diverse aspects of life. Over 20 classes of lncRNAs have been identified in bacteria and bacteriophages through comparative genomics analyses, but their biological functions remain largely unexplored. Due to the large sizes, the structural determinants of most lncRNAs also remain uncharacterized. Here we report the structures of two natural RNA nanocages formed by the lncRNA ROOL (rumen-originating, ornate, large) found in bacterial and phage genomes. ~2.9 Å cryo-electron microscopy (cryo-EM) structures reveal that ROOL RNAs form an octameric nanocage with a 28-nm diameter and 20-nm axial length, whose hollow inside features poorly ordered regions. The octamer is stabilized by numerous tertiary and quaternary interactions, including triple-strand A-minors that we propose to name "A-minor staples". The structure of an isolated ROOL monomer at ~3.2-Å resolution indicates that nanocage assembly involves a strand-swapping mechanism resulting in quaternary kissing loops. Finally, we show that ROOL RNA fused to an RNA aptamer, tRNA, or microRNA retains its structure forming a nanocage with radially displayed cargos. Our findings therefore may enable the engineering of novel RNA nanocages as delivery vehicles for research and therapeutic applications.
History
DepositionMar 21, 2025-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49873.png

Downloads & links

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Map

FileDownload / File: emd_49873.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å		0.83 Å/pix.
x 512 pix.
= 424.96 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.31
Minimum - Maximum-0.14216799 - 26.663235
Average (Standard dev.)-0.0052829627 (±0.4898231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_49873_additional_1.map
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Half map: #1

Fileemd_49873_half_map_1.map
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Half map: #2

Fileemd_49873_half_map_2.map
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Sample components

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Entire : ROOLfirm-tetramer

EntireName: ROOLfirm-tetramer
Components
  • Organelle or cellular component: ROOLfirm-tetramer
    • RNA: ROOLefa-tetramer

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Supramolecule #1: ROOLfirm-tetramer

SupramoleculeName: ROOLfirm-tetramer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Firmicutes bacterium CAG:227 (bacteria)

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Macromolecule #1: ROOLefa-tetramer

MacromoleculeName: ROOLefa-tetramer / type: rna / ID: 1
Source (natural)Organism: Firmicutes bacterium CAG:227 (bacteria)
SequenceString: UAUUUGAAUC AUACCUGCGA UCAACUCGAU GAAUAAAGUA CGCCAGUACU UCGAGGUGUG UGGUAAAUCC AAUAGACCCG GAAACGGGUG AGGGGCGCCC AGUCAACCAA AUCAAGGAUA CUUCUUUUGG AAGGCUGCCG GGGUUUAGUG AUAAAUCCCG GGAAGACGGA ...String:
UAUUUGAAUC AUACCUGCGA UCAACUCGAU GAAUAAAGUA CGCCAGUACU UCGAGGUGUG UGGUAAAUCC AAUAGACCCG GAAACGGGUG AGGGGCGCCC AGUCAACCAA AUCAAGGAUA CUUCUUUUGG AAGGCUGCCG GGGUUUAGUG AUAAAUCCCG GGAAGACGGA AACCGUCAAC GGAAACACAU AUCGCAGAAA UGCCCGCAUU UAAAAGCACG GAACUUCUGG AUGCAGCAAU AGACGCCUAC GGUGUAGGAG UAAGCCUAAG GGGUAUCAGU GUGGCAACUG AUAUGACAGA GGUAAAGCCA ACAAUGCAUU CUGCCUUGAU GACGGAGAAA UCCGCCUAUA ACAGAAGUCG CCGGUGAAAG UAGCCAUAUG GCAGAUUGAC AAAAACUCGU UUAUUAAUCU GAAUGGACGG UGAAAUUUAC AGGUAGCCAA UCCUGUGCAG GCUUGUGGCG UAAGCCAAGG GUAAGAAGUU AGGGGUCGCU CCCCGAAGCU CAGACUUAUC UUCCUGGUGG CAGAAUAUAA GUGAAGGGCA CGGAUUGUAC GGCGAAGGCC GGAUCGUAGG UAUGAUUCAA

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 51.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 44129
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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