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- EMDB-48389: ROOLfirm-octamer-wild type -

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Basic information

Entry
Database: EMDB / ID: EMD-48389
TitleROOLfirm-octamer-wild type
Map data
Sample
  • Organelle or cellular component: lncRNA-ROOL1-octamer
    • RNA: RNA (523-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
Keywordsnatural RNA nanocage / cryo-EM / drug delivery / RNA
Biological speciesFirmicutes bacterium CAG:227 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsLing XB / Ma JB / Fang WW / 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. Owing 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 ROOL (rumen-originating, ornate, large) lncRNA found in bacterial and phage genomes. The cryo-electron microscopy (cryo-EM) structures at 2.9-Å resolution reveal that ROOL RNAs form an octameric nanocage with a diameter of 28 nm and an axial length of 20 nm, in which the hollow inside features poorly ordered regions. The octamer is stabilized by numerous tertiary and quaternary interactions, including triple-strand A-minors, for which we propose the term '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, transfer RNA or microRNA retains its structure, forming a nanocage with radially displayed cargoes. Our findings, therefore, may enable engineering of novel RNA nanocages as delivery vehicles for research and therapeutic applications.
History
DepositionDec 20, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48389.png

Downloads & links

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Map

FileDownload / File: emd_48389.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
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.54
Minimum - Maximum-0.4348947 - 38.695880000000002
Average (Standard dev.)0.04534292 (±0.8953806)
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: #2

Fileemd_48389_additional_1.map
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Additional map: #1

Fileemd_48389_additional_2.map
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Half map: #2

Fileemd_48389_half_map_1.map
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Half map: #1

Fileemd_48389_half_map_2.map
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Sample components

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Entire : lncRNA-ROOL1-octamer

EntireName: lncRNA-ROOL1-octamer
Components
  • Organelle or cellular component: lncRNA-ROOL1-octamer
    • RNA: RNA (523-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION

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Supramolecule #1: lncRNA-ROOL1-octamer

SupramoleculeName: lncRNA-ROOL1-octamer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Firmicutes bacterium CAG:227 (bacteria)

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Macromolecule #1: RNA (523-MER)

MacromoleculeName: RNA (523-MER) / type: rna / ID: 1 / Number of copies: 8
Source (natural)Organism: Firmicutes bacterium CAG:227 (bacteria)
Molecular weightTheoretical: 187.716484 KDa
SequenceString: UAUUUGAAUC AUACCUGCGA UCAACUCGAU GAAUAAAGUA CGCCAGUACU UCGAGGUGUG UGGUAAAUCC AAUAGACCCG GAAACGGGU GAGGGGCGCC CAGUCAACCA AAUCAAGGAU ACUUCUUUUG GAAGGCUGCC GGGGUUUAGU GAUAAAUCCC G GGAAGACG ...String:
UAUUUGAAUC AUACCUGCGA UCAACUCGAU GAAUAAAGUA CGCCAGUACU UCGAGGUGUG UGGUAAAUCC AAUAGACCCG GAAACGGGU GAGGGGCGCC CAGUCAACCA AAUCAAGGAU ACUUCUUUUG GAAGGCUGCC GGGGUUUAGU GAUAAAUCCC G GGAAGACG GAAACCGUCA ACGGAAACAC AUAUCGCAGA AAUGCCCGCA UUUAAAAGCA CGGAACUUCU GGAUGCAGCA AU AGACGCC UACGGUGUAG GAGUAAGCCU AAGGGGUAUC AGUGUGGCAA CUGAUAUGAC AGAGGUAAAG CCAACAAUGC AUU CUGCCU UGAUGACGGA GAAAUCCGCC UAUAACAGAA GUCGCCGGUG AAAGUAGCCA UAUGGCAGAU UGACAAAAAC UCGU UUAUU AAUCUGAAUG GACGGUGAAA UUUACAGGUA GCCAAUCCUG UGCAGGCUUG UGGCGUAAGC CAAGGGUAAG AAGUU AGGG GUCGCUCCCC GAAGCUCAGA CUUAUCUUCC UGGUGGCAGA AUAUAAGUGA AGGGCACGGA UUGUACGGCG AAGGCC GGA UCGUAGGUAU GAUUCAA

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 41 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 56 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 420040
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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