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- EMDB-63100: Focused asymmetric unit of Env38-Golld RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-63100
TitleFocused asymmetric unit of Env38-Golld RNA
Map dataFocused asymmetric unit of Env38-Golld RNA
Sample
  • Complex: Focused asymmetric unit of Env38-Golld RNA
    • RNA: Env38-Golld RNA
KeywordsNatural RNA nanocages / large RNA / cryo-EM / Golld RNA / RNA
Biological speciesuncultured Caudovirales phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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 12, 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_63100.png

Downloads & links

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Map

FileDownload / File: emd_63100.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused asymmetric unit of Env38-Golld RNA
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å		1.06 Å/pix.
x 512 pix.
= 542.72 Å

Surface

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.80513114 - 1.3123956
Average (Standard dev.)0.00090808264 (±0.013560988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_63100_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Half map: Half map 1

Fileemd_63100_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_63100_half_map_2.map
AnnotationHalf map 2
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 : Focused asymmetric unit of Env38-Golld RNA

EntireName: Focused asymmetric unit of Env38-Golld RNA
Components
  • Complex: Focused asymmetric unit of Env38-Golld RNA
    • RNA: Env38-Golld RNA

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Supramolecule #1: Focused asymmetric unit of Env38-Golld RNA

SupramoleculeName: Focused asymmetric unit of Env38-Golld RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: uncultured Caudovirales phage (virus)
Molecular weightTheoretical: 3.8 MDa

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Macromolecule #1: Env38-Golld RNA

MacromoleculeName: Env38-Golld RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: uncultured Caudovirales phage (virus)
Molecular weightTheoretical: 268.889344 KDa
SequenceString: GGAUGGCCGC CUAUGGUCGU CAAAUAAACU ACGAAAGUAG GAUAAAGUGG AAUAGUAAGG UUUAGCUAUU CUGCGGUUUC AUCUUGUAA AGAUGGAGCU UGAGUAGGCA AGUGAGAUAU CAAUUUUUCU UAGUAUGUGA GGGUAACACU UUAGCAGAGG A GAAAAGUU ...String:
GGAUGGCCGC CUAUGGUCGU CAAAUAAACU ACGAAAGUAG GAUAAAGUGG AAUAGUAAGG UUUAGCUAUU CUGCGGUUUC AUCUUGUAA AGAUGGAGCU UGAGUAGGCA AGUGAGAUAU CAAUUUUUCU UAGUAUGUGA GGGUAACACU UUAGCAGAGG A GAAAAGUU GACUGGGUCU UUGCAGAGAU UCAGUUGAGU UCGGAAGAGC AAUAAGAAUA ACUCAUAGAA UUCAAUGCGA GA GGUAGGG AACUAAUCCC UCCCUAUAAU CGCGGUAUUC AAUAUGAUAG UUUACUUAAC AUCAAAUUGG GGAAACCCUU UAA GAUAAG AUAGUGUACG GGUGGUGCCG UUAUUAUCCU UUGAUAGAGU GUACCAGCAC CUAUCGAUGA AGUAAACUUG GAAU AUGGU GGUAGGGAUA CCACAUCGGG UAGUUAAGUA UUCUGUCGUU CAAAAGGCGG CGGAGCUUGU GAUAGACCGC UACCU GAAA CCACUGCAAA ACCAAACUUA UAUUUGCAUU UAGGAUUGCA AAAUCAUAAA AAUCAAAAUA AGAAAAAGUG UCUAUC AGU UUUGACCGAA AGGUGUCUAC AUAGUAAUGA GUUGUUCAUU GCCACAAACA CUCUCAAGGU GAAUGUGAUU CUUUCGA AA GGUUUCUAAC ACCGCAAGUG UGAAUCUGCU CGGCAGGGUA GAAGAAAAUA AGUAAGAAGA GAGUAGGUUA AAACUCAA A GAGUGGUUCA CUUAAAUAAC CGACAUUGGU UGUUACAUCU CAAAAGGAUG UGGAAACAAA GGGAAUAGAU AAUCCUUUU AAAGACAACU ACAAUAUGGU GUAUUCUCAG CCU

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5894560
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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