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- EMDB-48386: ROOLefa-octamer-wild type -

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Basic information

Entry
Database: EMDB / ID: EMD-48386
TitleROOLefa-octamer-wild type
Map datalncRNA-ROOL2-octamer
Sample
  • Organelle or cellular component: lncRNA-ROOL2-octamer
    • RNA: RNA (526-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION
Keywordsnatural RNA nanocage / drug delivery / RNA
Biological speciesEnterococcus faecalis JH1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.94 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. 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48386.png

Downloads & links

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Map

FileDownload / File: emd_48386.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationlncRNA-ROOL2-octamer
Projections & slices

Image control

Size
Brightness
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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: 3.24
Minimum - Maximum-0.19249544 - 37.004530000000003
Average (Standard dev.)0.043293063 (±0.8669108)
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: Additional Map B

Fileemd_48386_additional_1.map
AnnotationAdditional Map B
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Additional map: Additional Map A

Fileemd_48386_additional_2.map
AnnotationAdditional Map A
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Half map: Half Map B

Fileemd_48386_half_map_1.map
AnnotationHalf Map B
Projections & Slices
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Half map: Half Map A

Fileemd_48386_half_map_2.map
AnnotationHalf Map A
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Sample components

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Entire : lncRNA-ROOL2-octamer

EntireName: lncRNA-ROOL2-octamer
Components
  • Organelle or cellular component: lncRNA-ROOL2-octamer
    • RNA: RNA (526-MER)
  • Ligand: POTASSIUM ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: lncRNA-ROOL2-octamer

SupramoleculeName: lncRNA-ROOL2-octamer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Enterococcus faecalis JH1 (bacteria)

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Macromolecule #1: RNA (526-MER)

MacromoleculeName: RNA (526-MER) / type: rna / ID: 1 / Number of copies: 8
Source (natural)Organism: Enterococcus faecalis JH1 (bacteria)
Molecular weightTheoretical: 187.837453 KDa
SequenceString: AAUUGAAAAA UCAAUAGAUU UAAACCUAGU GAAGAGCAUU UGAACAAUGU GCUAGGGUAG UAUGGGAUAA GUCGAUAACU AAAAUGAAU UGGGAUACUG AUUGAUUUUA GUGGUGGAUU UUACAGCAAU GUAAAAAGGA CUAAUAGUAA AAGCUAUUAA U CGCAAAGU ...String:
AAUUGAAAAA UCAAUAGAUU UAAACCUAGU GAAGAGCAUU UGAACAAUGU GCUAGGGUAG UAUGGGAUAA GUCGAUAACU AAAAUGAAU UGGGAUACUG AUUGAUUUUA GUGGUGGAUU UUACAGCAAU GUAAAAAGGA CUAAUAGUAA AAGCUAUUAA U CGCAAAGU ACUACGUGGA AUUUGUGCAG GUGUAAGGUA CGAAACUUUC GAGUGUGACA AUAGACGCUC CAGUGGAGAA UA AUCUAAG UUAGGUGGAA GUGUGAGAAG CUUGGCAGAC CUUAGAAAAC UCAAACCAAG CGCUUUGCAG AGAAACUGAG AAA UCAGUG UUUAACGAAA GAAGUCGGUA CGAGUAGCUU AAUGCAGCAA UUUAUUUACA GAUGACAAAU AAUAAAAAUG GGAC UCUUA UGUAAAUGCU GAAUGUUCAA GUGAAAGUUA UUAGCCAGUA GAGCUAGAUC AUACAGAAAA AGCAAAGAGA AGCUA UUGG GUAGCGCCCG AUAGUUCAGC CUCUUUGGGU AUGUGACUGA AUAACACUGU AAACAAAGGA AGCAGGAAGA AAAGCC UAA AUCUGUUGAU UUUUGAG

GENBANK: GENBANK: CP060804.1

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 43 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 11 / Formula: MG
Molecular weightTheoretical: 24.305 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: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225901
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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