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- EMDB-48214: GOLLD RNA nanocage (env-38) -

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Basic information

Entry
Database: EMDB / ID: EMD-48214
TitleGOLLD RNA nanocage (env-38)
Map dataComposite reconstruction of GOLLD RNA nanocage.
Sample
  • Complex: GOLLD RNA nanocage (env-38)
    • RNA: GOLLD RNA nanocage
KeywordsGOLLD / nanocage / ncRNA / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKretsch RC / Wu Y / Nye G / Das R / Chiu W
Funding support United States, 4 items
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: Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate ...Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 Å. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. 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, empty except for a disordered loop. Extensive intra- 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 6, 2024-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48214.png

Downloads & links

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Map

FileDownload / File: emd_48214.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite reconstruction of GOLLD RNA nanocage.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.38 Å/pix.
x 500 pix.
= 688. Å		1.38 Å/pix.
x 500 pix.
= 688. Å		1.38 Å/pix.
x 500 pix.
= 688. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.376 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-68.507720000000006 - 143.899290000000008
Average (Standard dev.)0.018259076 (±2.532389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 688.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map of composite reconstruction of GOLLD RNA nanocage.

Fileemd_48214_half_map_1.map
AnnotationHalf-map of composite reconstruction of GOLLD RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of composite reconstruction of GOLLD RNA nanocage.

Fileemd_48214_half_map_2.map
AnnotationHalf-map of composite reconstruction of GOLLD RNA nanocage.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GOLLD RNA nanocage (env-38)

EntireName: GOLLD RNA nanocage (env-38)
Components
  • Complex: GOLLD RNA nanocage (env-38)
    • RNA: GOLLD RNA nanocage

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Supramolecule #1: GOLLD RNA nanocage (env-38)

SupramoleculeName: GOLLD RNA nanocage (env-38) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.768 MDa

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Macromolecule #1: GOLLD RNA nanocage

MacromoleculeName: GOLLD RNA nanocage / type: rna / ID: 1 / Number of copies: 14
Source (natural)Organism: synthetic construct (others)
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

Concentration2.1 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
50.0 mMSodium HEPES
10.0 mMMagnesium ChlorideMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 23281 / Average exposure time: 2.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2669865
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-uniform Refinement / Number images used: 20375
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Ab Initio reconstruction multiclass
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-uniform Refinement
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9mee:
GOLLD RNA nanocage (env-38)

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