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- EMDB-63029: Composite map of Sag-18RS21-tRNASer Golld RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-63029
TitleComposite map of Sag-18RS21-tRNASer Golld RNA
Map dataComposite map of Sag-18RS21-tRNASer Golld RNA
Sample
  • Complex: Composite map of Sag-18RS21-tRNASer Golld RNA
    • RNA: Sag-18RS21-tRNASer Golld RNA
KeywordsNatural RNA nanocages / large RNA / cryo-EM / Golld RNA / RNA
Biological speciesStreptococcus agalactiae 18RS21 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsZhang K / Li S
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
DepositionJan 7, 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_63029.png

Downloads & links

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Map

FileDownload / File: emd_63029.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of Sag-18RS21-tRNASer Golld RNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-42.988124999999997 - 70.449820000000003
Average (Standard dev.)0.026721979 (±1.7487047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Composite map of Sag-18RS21-tRNASer Golld RNA

EntireName: Composite map of Sag-18RS21-tRNASer Golld RNA
Components
  • Complex: Composite map of Sag-18RS21-tRNASer Golld RNA
    • RNA: Sag-18RS21-tRNASer Golld RNA

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Supramolecule #1: Composite map of Sag-18RS21-tRNASer Golld RNA

SupramoleculeName: Composite map of Sag-18RS21-tRNASer Golld RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Streptococcus agalactiae 18RS21 (bacteria)
Molecular weightTheoretical: 1.45 MDa

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Macromolecule #1: Sag-18RS21-tRNASer Golld RNA

MacromoleculeName: Sag-18RS21-tRNASer Golld RNA / type: rna / ID: 1 / Number of copies: 10
Source (natural)Organism: Streptococcus agalactiae 18RS21 (bacteria)
Molecular weightTheoretical: 153.776844 KDa
SequenceString: GGAGUAGGCG UUGCGCAUUU UGUUGCUCAA AAGGCGACGA AACGCAAGGC AAUGCACGUC UGCGAUACAC GAAAACAAUG CUAUUUGUU GAAAAUAUUG GAAUAAAGCA AAAGUCAUUG CCCGUCGCAA ACGAAAGUGU GCUUCGGUAG CUAGGCUACC U GCUAGAGU ...String:
GGAGUAGGCG UUGCGCAUUU UGUUGCUCAA AAGGCGACGA AACGCAAGGC AAUGCACGUC UGCGAUACAC GAAAACAAUG CUAUUUGUU GAAAAUAUUG GAAUAAAGCA AAAGUCAUUG CCCGUCGCAA ACGAAAGUGU GCUUCGGUAG CUAGGCUACC U GCUAGAGU CUCGCAAGGA UAAUAGCAAA GUCAAAGAGU AAAGCAGCUU AGACCUUUAG CGGGGUUUUC GUUAAUUGAA AA AUGGCUU AGUAGUUUGC GGCGUAACGA GUGGUUAGCG AUACUAACCG CGCAUGGUUG UUACUUGAAG GGAUUUGAGU GGA UAAAAA ACUAAAACAU AAGGUUUUGA AAGACAACUG ACUAAACGUG UAAUCUCAGC GUAUUUGCAU UUGGAAAGUU ACUC AAGUG GUUUAAGAGG ACAGGUUGCU ACCUUGUUAG GCGUGUAAAA GCGUGCGUGG GUUCGAAUCC UACACUUUCU A

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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 (6k x 4k) / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 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: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1296920
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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