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- EMDB-70248: Focused refinement of 5' domain of a single subunit of GOLLD RNA ... -

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Basic information

Entry
Database: EMDB / ID: EMD-70248
TitleFocused refinement of 5' domain of a single subunit of GOLLD RNA nanocage.
Map dataReconstruction of GOLLD RNA nanocage single subunit focused refinement.
Sample
  • Complex: GOLLD RNA nanocage (env-38)
    • RNA: GOLLD RNA
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)R35 GM122579 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129541 United States
National Science Foundation (NSF, United States)2330652 United States
Citation
Journal: 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: The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron ...The structures of natural RNAs remain poorly characterized and may hold numerous surprises. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryo-electron microscopy (cryo-EM). GOLLD (Giant, Ornate, Lake- and Lactobacillales-Derived), ROOL (Rumen-Originating, Ornate, Large) and OLE (Ornate Large Extremophilic) RNAs form homo-oligomeric complexes whose stoichiometries are retained at lower concentrations than measured in cells. 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, each empty except for a disordered loop. Extensive intramolecular 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.
#1: Journal: BioRxiv / Year: 2025
Title: Naturally ornate RNA-only complexes revealed by cryo-EM
Authors: Kretsch RC / Wu Y / Shabalina SA / Lee H / Nye G / Koonin E / Gao A / Chiu W / Das R
History
DepositionApr 17, 2025-
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_70248.png

Downloads & links

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Map

FileDownload / File: emd_70248.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of GOLLD RNA nanocage single subunit focused refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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: 0.3
Minimum - Maximum-0.5413284 - 1.8135657
Average (Standard dev.)0.0010471934 (±0.034196433)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Mask #1

Fileemd_70248_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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Half map: Half map for GOLLD RNA nanocage single subunit focused refinement.

Fileemd_70248_half_map_1.map
AnnotationHalf map for GOLLD RNA nanocage single subunit focused refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map for GOLLD RNA nanocage single subunit focused refinement.

Fileemd_70248_half_map_2.map
AnnotationHalf map for GOLLD RNA nanocage single subunit focused refinement.
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

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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

MacromoleculeName: GOLLD RNA / type: rna / ID: 1
Source (natural)Organism: synthetic construct (others)
SequenceString: GGAUGGCCGC CUAUGGUCGU CAAAUAAACU ACGAAAGUAG GAUAAAGUGG AAUAGUAAGG UUUAGCUAUU CUGCGGUUUC AUCUUGUAAA GAUGGAGCUU GAGUAGGCAA GUGAGAUAUC AAUUUUUCUU AGUAUGUGAG GGUAACACUU UAGCAGAGGA GAAAAGUUGA ...String:
GGAUGGCCGC CUAUGGUCGU CAAAUAAACU ACGAAAGUAG GAUAAAGUGG AAUAGUAAGG UUUAGCUAUU CUGCGGUUUC AUCUUGUAAA GAUGGAGCUU GAGUAGGCAA GUGAGAUAUC AAUUUUUCUU AGUAUGUGAG GGUAACACUU UAGCAGAGGA GAAAAGUUGA CUGGGUCUUU GCAGAGAUUC AGUUGAGUUC GGAAGAGCAA UAAGAAUAAC UCAUAGAAUU CAAUGCGAGA GGUAGGGAAC UAAUCCCUCC CUAUAAUCGC GGUAUUCAAU AUGAUAGUUU ACUUAACAUC AAAUUGGGGA AACCCUUUAA GAUAAGAUAG UGUACGGGUG GUGCCGUUAU UAUCCUUUGA UAGAGUGUAC CAGCACCUAU CGAUGAAGUA AACUUGGAAU AUGGUGGUAG GGAUACCACA UCGGGUAGUU AAGUAUUCUG UCGUUCAAAA GGCGGCGGAG CUUGUGAUAG ACCGCUACCU GAAACCACUG CAAAACCAAA CUUAUAUUUG CAUUUAGGAU UGCAAAAUCA UAAAAAUCAA AAUAAGAAAA AGUGUCUAUC AGUUUUGACC GAAAGGUGUC UACAUAGUAA UGAGUUGUUC AUUGCCACAA ACACUCUCAA GGUGAAUGUG AUUCUUUCGA AAGGUUUCUA ACACCGCAAG UGUGAAUCUG CUCGGCAGGG UAGAAGAAAA UAAGUAAGAA GAGAGUAGGU UAAAACUCAA AGAGUGGUUC ACUUAAAUAA CCGACAUUGG UUGUUACAUC UCAAAAGGAU GUGGAAACAA AGGGAAUAGA UAAUCCUUUU 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
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Local 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

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