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- EMDB-48163: OLE RNA dimer (Clostridium acetobutylicum) -

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Basic information

Entry
Database: EMDB / ID: EMD-48163
TitleOLE RNA dimer (Clostridium acetobutylicum)
Map dataC2 reconstruction of OLE dimer.
Sample
  • Complex: OLE RNA dimer - Clostridium acetobutylicum
    • RNA: OLE RNA dimer
KeywordsOLE / ncRNA / RNA
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKretsch RC / Wu Y / Das R / Chiu W / Zhang K
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: 2024
Title: Naturally ornate RNA-only complexes revealed by cryo-EM
Authors: Kretsch RC / Wu Y / Shabalina SA / Lee H / Nye G / Koonin EV / Gao A / Chiu W / Das R
History
DepositionDec 5, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48163.png

Downloads & links

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Map

FileDownload / File: emd_48163.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC2 reconstruction of OLE dimer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.95 Å/pix.
x 360 pix.
= 343.44 Å		0.95 Å/pix.
x 360 pix.
= 343.44 Å		0.95 Å/pix.
x 360 pix.
= 343.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.954 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-23.949169999999999 - 51.959933999999997
Average (Standard dev.)0.000000000002625 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 343.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: C1 reconstruction of OLE dimer.

Fileemd_48163_additional_1.map
AnnotationC1 reconstruction of OLE dimer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of OLE dimer (C2).

Fileemd_48163_half_map_1.map
AnnotationHalf-map of OLE dimer (C2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map of OLE dimer (C2).

Fileemd_48163_half_map_2.map
AnnotationHalf-map of OLE dimer (C2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : OLE RNA dimer - Clostridium acetobutylicum

EntireName: OLE RNA dimer - Clostridium acetobutylicum
Components
  • Complex: OLE RNA dimer - Clostridium acetobutylicum
    • RNA: OLE RNA dimer

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Supramolecule #1: OLE RNA dimer - Clostridium acetobutylicum

SupramoleculeName: OLE RNA dimer - Clostridium acetobutylicum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)
Molecular weightTheoretical: 373 KDa

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Macromolecule #1: OLE RNA dimer

MacromoleculeName: OLE RNA dimer / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)
Molecular weightTheoretical: 186.321078 KDa
SequenceString: GGUGCAGUAU UCUAGUCAGG GAAAUGCUUU UUGAAGGCGG GGCUAAAAAU CCGCUAAAGG GCACAUCGAU GAAGUUCCUG GUGCUGGCC UUAGAAUGCC CAGUCUUGGG CUUGUGCUGG GAGUUAAAAA AGCUGGGGCA CUCGCAAUGG CAUGCGACAA A UGACCCUA ...String:
GGUGCAGUAU UCUAGUCAGG GAAAUGCUUU UUGAAGGCGG GGCUAAAAAU CCGCUAAAGG GCACAUCGAU GAAGUUCCUG GUGCUGGCC UUAGAAUGCC CAGUCUUGGG CUUGUGCUGG GAGUUAAAAA AGCUGGGGCA CUCGCAAUGG CAUGCGACAA A UGACCCUA CUUUUGUGGA GGCCAAUUAU UGUAUAUUGA GAGAGAUAUU CAAUAUACGA AAUUGGGGUA AACCUGCAAU GU GGUGUAA AAGCUAUGUG CAGUGUAGCC UGCCUUGAGU GGUAUGGGGA GAGGAGAUAA ACAAGUCAAA AAUUUUAGGC CUA AGUUUU UGUACUAUUG AACUCUGAAA CCUAUGUUGC AAAAGAGGCU AAGAAAGCAU CUAACUGUUG AGGAAAACUC CUAG ACUGU UUUGGUAAAA UGAGGAUUGC AGUGCGGACU UAGUGGCAAU UCAGUCCUGA AAGUGGCAAC ACUUCAGCUC GGAUA UUAA AGGGAAACCG CUAUAUGGCG ACGUAUAGUU AUUCGUGGGG AAAGCCUACU GAACCUAUGC CGUAAGAUUU ACUUAU UUU GUUACCACAU UGCC

GENBANK: GENBANK: AE001437.1

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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

Concentration2.8 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: 15 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: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 6752 / Average exposure time: 4.74 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: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
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: 541108
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: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: Non-uniform Refinement / Number images used: 87716
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-9mcw:
OLE RNA dimer (Clostridium acetobutylicum)

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