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- PDB-9le3: Consensus map of UCC118 Rool RNA -

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Basic information

Entry
Database: PDB / ID: 9le3
TitleConsensus map of UCC118 Rool RNA
ComponentsUCC118 Rool RNA
KeywordsRNA / Natural RNA nanocages / large RNA / cryo-EM / Rool
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesLigilactobacillus salivarius UCC118 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsZhang, K. / Li, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural insights into higher-order natural RNA-only multimers.
Authors: Shengchun Zhang / Ran Yi / Linfeng An / Ji Liu / Xuebiao Yao / Shanshan Li / Kaiming Zhang /
Abstract: RNA-only complexes adopt intricate three-dimensional structures to fulfill diverse functions independently of protein partners. Although multimeric RNA-only structures have been engineered in ...RNA-only complexes adopt intricate three-dimensional structures to fulfill diverse functions independently of protein partners. Although multimeric RNA-only structures have been engineered in synthetic RNA nanomaterials, naturally occurring RNA-only complexes have primarily been observed as monomers or dimers, leaving higher-order assemblies largely unexplored. ROOL (rumen-originating, ornate, large) and GOLLD (giant, ornate, lake- and Lactobacillales-derived) RNAs are conserved non-coding RNAs with complex secondary structures, but their high-resolution architectures remain unknown. Here, we determine the cryo-electron microscopy structures of UCC118-Rool RNA, Sag-Golld RNA and Env38-Golld RNA at 1.96-2.98 Å resolution, revealing their distinct hexameric, decameric and tetradecameric assemblies. These higher-order architectures are stabilized by an array of tertiary motifs such as kissing loops and tetraloop-receptor motifs, underscoring the conserved principles of RNA self-assembly. By elucidating the molecular details of these higher-order RNA-only assemblies, this study expands our understanding of RNA-based architectures and broadens the scope of RNA structural biology.
History
DepositionJan 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UCC118 Rool RNA
B: UCC118 Rool RNA
C: UCC118 Rool RNA
D: UCC118 Rool RNA
E: UCC118 Rool RNA
F: UCC118 Rool RNA


Theoretical massNumber of molelcules
Total (without water)1,006,2266
Polymers1,006,2266
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain
UCC118 Rool RNA


Mass: 167704.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ligilactobacillus salivarius UCC118 (bacteria)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 90821902
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: Consensus map of UCC118 Rool RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.9 MDa / Experimental value: NO
Source (natural)Organism: Ligilactobacillus salivarius UCC118 (bacteria)
Source (recombinant)Organism: in vitro transcription vector pT7-Fluc(deltai) (others)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 1500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 504297 / Symmetry type: POINT

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