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- EMDB-63679: Focused asymmetric unit of UCC118 Rool RNA at 1.96-angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-63679
TitleFocused asymmetric unit of UCC118 Rool RNA at 1.96-angstrom resolution
Map dataFocused asymmetric unit of UCC118 Rool RNA at 1.96-angstrom resolution
Sample
  • Complex: UCC118 Rool RNA monomer
    • RNA: UCC118 Rool RNA monomer
KeywordsNatural RNA-Only Multimer / cryo-EM / Oligomer / Rool. / RNA
Biological speciesLigilactobacillus salivarius UCC118 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.96 Å
AuthorsZhang S / Yi R / An L / Li S / Zhang K
Funding support China, 1 items
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
DepositionMar 10, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63679.png

Downloads & links

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Map

FileDownload / File: emd_63679.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused asymmetric unit of UCC118 Rool RNA at 1.96-angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.58 Å/pix.
x 512 pix.
= 294.4 Å		0.58 Å/pix.
x 512 pix.
= 294.4 Å		0.58 Å/pix.
x 512 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.575 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.10673096 - 0.3109799
Average (Standard dev.)0.0003796938 (±0.005675442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Refined map by ResolveCryoEM in phenix.

Fileemd_63679_additional_1.map
AnnotationRefined map by ResolveCryoEM in phenix.
Projections & Slices
AxesZYX

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Additional map: Unsharpened map

Fileemd_63679_additional_2.map
AnnotationUnsharpened map
Projections & Slices
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Half map: Half map A

Fileemd_63679_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_63679_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : UCC118 Rool RNA monomer

EntireName: UCC118 Rool RNA monomer
Components
  • Complex: UCC118 Rool RNA monomer
    • RNA: UCC118 Rool RNA monomer

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Supramolecule #1: UCC118 Rool RNA monomer

SupramoleculeName: UCC118 Rool RNA monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Ligilactobacillus salivarius UCC118 (bacteria)

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Macromolecule #1: UCC118 Rool RNA monomer

MacromoleculeName: UCC118 Rool RNA monomer / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Ligilactobacillus salivarius UCC118 (bacteria)
Molecular weightTheoretical: 167.70425 KDa
SequenceString: GGACCGAUGA AGCUAGUGGA UGAGGUGUGA CAAGCCGCCU AGCCAUACGA CUCUUAAUAA CUACUAUGAC GAAAUAUACG GAUACGUUU AUUUUUUCUA AUUUCCACUU GGGUAGUACU AAUUGGGAGC AACGAAAAAA GUUGUGUAGA GAGAAGCAAG G GGACUCAU ...String:
GGACCGAUGA AGCUAGUGGA UGAGGUGUGA CAAGCCGCCU AGCCAUACGA CUCUUAAUAA CUACUAUGAC GAAAUAUACG GAUACGUUU AUUUUUUCUA AUUUCCACUU GGGUAGUACU AAUUGGGAGC AACGAAAAAA GUUGUGUAGA GAGAAGCAAG G GGACUCAU AUCUGAAACU AAGACACUUG CCGUCAGGGA UUCGCAAUAU GCCAUCUUCA GUUAAUUAAG GCUGAUUACC UU AGGAACC AAAAGAAGAA UAUCAACUAA GAAUUCGUGU CGUGAAGUUG UGGUGACGCA ACUAUAACUG ACGAGUAAGG UUU GAGUAG CCAAAAUCGA CAAUCUUACA UUAACUGGAA CAUUGCACAU GUUUGGUGAA AAUUGGAUAG GAAAAGAUCU AUGC CCUGA ACUUGAAAUG CGGACUAGGU CGUGGAAGUU GCUAGCCAUG AUGUGCUAGU CUGAUUCAGU AGUCUAAUAA GUCCA GAUA CAAGAGUAUC CCACGUAAGC CAAUACGCGU CGGUUU

GENBANK: GENBANK: CP000234.1

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 36386 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5687172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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