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

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Basic information

Entry
Database: PDB / ID: 9mds
TitleROOL RNA nanocage (env-120)
ComponentsRNA (598-MER)
KeywordsRNA / ROOL / ncRNA / nanocage
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKretsch, R.C. / Wu, Y. / Das, R. / Chiu, W.
Funding support United States, 4items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (598-MER)
B: RNA (598-MER)
C: RNA (598-MER)
D: RNA (598-MER)
E: RNA (598-MER)
F: RNA (598-MER)
G: RNA (598-MER)
H: RNA (598-MER)


Theoretical massNumber of molelcules
Total (without water)1,624,5778
Polymers1,624,5778
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain
RNA (598-MER)


Mass: 203072.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ROOL RNA nanocage / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.702 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMSodium HEPES1
210 mMMagnesium chlorideMgCl21
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.42 sec. / Electron dose: 59 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 4462
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selectionTempalte Picker
2cryoSPARC4.5.3particle selection2D class
3EPU3.5image acquisition
5cryoSPARC4.5.3CTF correction
8RELION5model fittingModelAngelo
9Rosetta3.1model fittingDRRAFTER
11cryoSPARC4.5.3initial Euler assignmentab initio reconstruction multi class
12cryoSPARC4.5.3final Euler assignmentHomogeneous refinement
14cryoSPARC4.5.33D reconstructionLocal refinement
15Rosetta3.1model refinementERRRASER2
16Coot0.9.8model refinement
17PHENIX1.21model refinementreal_space_refine
18ISOLDE1.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 71114
SymmetryPoint symmetry: D4 (2x4 fold dihedral)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31056 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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