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- EMDB-48179: ROOL RNA nanocage (env-120) -

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Basic information

Entry
Database: EMDB / ID: EMD-48179
TitleROOL RNA nanocage (env-120)
Map dataComposite reconstruction of ROOL RNA nanocage.
Sample
  • Complex: ROOL RNA nanocage
    • RNA: RNA (598-MER)
KeywordsROOL / RNA / ncRNA / nanocage
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKretsch RC / Wu Y / Das R / Chiu W
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
National Science Foundation (NSF, United States)2330652 United States
CitationJournal: Nature / Year: 2025
Title: Naturally ornate RNA-only complexes revealed by cryo-EM.
Authors: Rachael C Kretsch / Yuan Wu / Svetlana A Shabalina / Hyunbin Lee / Grace Nye / Eugene V Koonin / Alex Gao / Wah Chiu / Rhiju Das /
Abstract: The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron ...The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, each empty except for a disordered loop. Extensive intramolecular and intermolecular A-minor interactions, kissing loops, an unusual A-A helix and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.
History
DepositionDec 5, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48179.png

Downloads & links

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Map

FileDownload / File: emd_48179.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite reconstruction of ROOL RNA nanocage.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.29 Å/pix.
x 400 pix.
= 516. Å		1.29 Å/pix.
x 400 pix.
= 516. Å		1.29 Å/pix.
x 400 pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-24.390419000000001 - 46.201050000000002
Average (Standard dev.)0.000000000003189 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 516.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: D4 reconstruction of ROOL RNA nanocage.

Fileemd_48179_additional_1.map
AnnotationD4 reconstruction of ROOL RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the bottom of one chain.

Fileemd_48179_additional_2.map
AnnotationFocused refinement of ROOL RNA of the bottom of one chain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the bottom of three chains.

Fileemd_48179_additional_3.map
AnnotationFocused refinement of ROOL RNA of the bottom of three chains.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the bottom left of one chain.

Fileemd_48179_additional_4.map
AnnotationFocused refinement of ROOL RNA of the bottom left of one chain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of one chain.

Fileemd_48179_additional_5.map
AnnotationFocused refinement of ROOL RNA of one chain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the bottom right of one chain.

Fileemd_48179_additional_6.map
AnnotationFocused refinement of ROOL RNA of the bottom right of one chain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the top of one chain.

Fileemd_48179_additional_7.map
AnnotationFocused refinement of ROOL RNA of the top of one chain.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: C1 reconstruction of ROOL RNA nanocage.

Fileemd_48179_additional_8.map
AnnotationC1 reconstruction of ROOL RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Focused refinement of ROOL RNA of the bottom of two chains.

Fileemd_48179_additional_9.map
AnnotationFocused refinement of ROOL RNA of the bottom of two chains.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map for composite reconstruction of ROOL RNA nanocage.

Fileemd_48179_half_map_1.map
AnnotationHalf-map for composite reconstruction of ROOL RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map for composite reconstruction of ROOL RNA nanocage.

Fileemd_48179_half_map_2.map
AnnotationHalf-map for composite reconstruction of ROOL RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ROOL RNA nanocage

EntireName: ROOL RNA nanocage
Components
  • Complex: ROOL RNA nanocage
    • RNA: RNA (598-MER)

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Supramolecule #1: ROOL RNA nanocage

SupramoleculeName: ROOL RNA nanocage / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 1.702 MDa

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Macromolecule #1: RNA (598-MER)

MacromoleculeName: RNA (598-MER) / type: rna / ID: 1 / Number of copies: 8
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 203.072094 KDa
SequenceString: GUUUAUAGAC AUAGCCUUGU GUAUGACUGU CUAAUCAACA GUGCAAGGAA UUAGUUGUGC UCUCAAAAGG AGUUAUGUGA AGGAAAGAU UAAAUGGAUA CAUUUAAUUA AGUACAAUUA CUACAAAAUC UAUAAUGACU GGGUAAGUCA CCCGUAAGAA G GAUGAGUU ...String:
GUUUAUAGAC AUAGCCUUGU GUAUGACUGU CUAAUCAACA GUGCAAGGAA UUAGUUGUGC UCUCAAAAGG AGUUAUGUGA AGGAAAGAU UAAAUGGAUA CAUUUAAUUA AGUACAAUUA CUACAAAAUC UAUAAUGACU GGGUAAGUCA CCCGUAAGAA G GAUGAGUU AGUAGAGAUA UAAUAAUAUC UUACAGUUCA ACUGAUGUGC AAGUUUAUAA GUAGACGUAG UGUGAAAGAC UU AUCGCUA ACGCAAUAGA CGUUAUCUCG AAAGGAUAAA AGAAACCAAG AAGAUAUACA AAUUGGUAAC UUGUAUAAGC CCU UGGUAA UACCAAAUAA GUUAGUUCCU CAUGAUGUCG UGGAAACAUG ACUAUAAGAU AAGUUGAAUU CGAUAGUAGC CCAA GAGGA AUC(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N) (N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N)(N)(N)(N)(N)(N)(N) (N)(N)(N)(N) (N)(UNK)GAU UGUGCCUUGA AAAAGGUGGG UGAGGUCUGU GGGUAAAAAU UAAUUCCCAU CUGGUUUUGG AUUUUCUUC GGAAAAUUGG UGCAAGAAGC GUGGAGUUGC UAACCAUUGC UCAGACUUGU AUCGCCAGUA GCACGAUAAC GAUAUUUAUG AAUGUUGUA AGGUGAAUAA AAGCCUAUGA UUUGUGAAC

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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

Concentration1.9 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMSodium HEPES
10.0 mMMagnesium chlorideMgCl2
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 4462 / Average exposure time: 1.42 sec. / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 71114
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Local refinement / Number images used: 31056
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: ab initio reconstruction multi class
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Homogeneous refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9mds:
ROOL RNA nanocage (env-120)

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