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- EMDB-48162: raiA RNA motif (Clostridium acetobutylicum) -

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Basic information

Entry
Database: EMDB / ID: EMD-48162
TitleraiA RNA motif (Clostridium acetobutylicum)
Map dataCryo-EM map of raiA RNA.
Sample
  • Complex: raiA RNA - Clostridium acetobutylicum
    • RNA: raiA RNA
KeywordsraiA / ncRNA / RNA
Biological speciesClostridium acetobutylicum ATCC 824 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKretsch RC / Wu Y / Nye G / 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: 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.
#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_48162.png

Downloads & links

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Map

FileDownload / File: emd_48162.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of raiA RNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.86 Å/pix.
x 320 pix.
= 276.544 Å		0.86 Å/pix.
x 320 pix.
= 276.544 Å		0.86 Å/pix.
x 320 pix.
= 276.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8642 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-64.414349999999999 - 95.918120000000002
Average (Standard dev.)-0.000000000004211 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 276.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of raiA RNA.

Fileemd_48162_half_map_1.map
AnnotationHalf map of raiA RNA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of raiA RNA.

Fileemd_48162_half_map_2.map
AnnotationHalf map of raiA RNA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : raiA RNA - Clostridium acetobutylicum

EntireName: raiA RNA - Clostridium acetobutylicum
Components
  • Complex: raiA RNA - Clostridium acetobutylicum
    • RNA: raiA RNA

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Supramolecule #1: raiA RNA - Clostridium acetobutylicum

SupramoleculeName: raiA RNA - Clostridium acetobutylicum / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)
Molecular weightTheoretical: 67 KDa

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Macromolecule #1: raiA RNA

MacromoleculeName: raiA RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Clostridium acetobutylicum ATCC 824 (bacteria)
Molecular weightTheoretical: 66.465438 KDa
SequenceString: GGUUAAGUUA GGUUUGUGGU UGAAAGUCGA UGCCAGUCGC AGGCAAAACG AUCCACGUAA GUUAAACAAA GUUUUAAUGA GCAUGGUGC GGCUUAGAAG UAAGUCCUGC CGCUUUAGGC GAGAGUAUUA GUAGUGAGAG GGUAAUUCCG GGUAGCGAAA C UUCCAGCA ...String:
GGUUAAGUUA GGUUUGUGGU UGAAAGUCGA UGCCAGUCGC AGGCAAAACG AUCCACGUAA GUUAAACAAA GUUUUAAUGA GCAUGGUGC GGCUUAGAAG UAAGUCCUGC CGCUUUAGGC GAGAGUAUUA GUAGUGAGAG GGUAAUUCCG GGUAGCGAAA C UUCCAGCA GGCGAGUGUG GGGUCAAAGA CCAGGUCAAC UAACUUA

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

Concentration1.3 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: 10825 / Average exposure time: 1.65 sec. / Average electron dose: 60.0 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 reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / 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: 318464
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-9ely:
raiA RNA motif (Clostridium acetobutylicum)

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