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- EMDB-51119: Cryo-EM structure of raiA ncRNA from Clostridium reveals a new RN... -

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Basic information

Entry
Database: EMDB / ID: EMD-51119
TitleCryo-EM structure of raiA ncRNA from Clostridium reveals a new RNA 3D fold
Map data
Sample
  • Cell: raiA ncRNA
    • RNA: raiA (224-MER)
KeywordsncRNA / raiA / RNA
Biological speciesClostridium sp. CAG:138 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsBadepally NG / Moura TR / Purta E / Baulin E / Bujnicki JM
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: J Mol Biol / Year: 2024
Title: Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold.
Authors: Nagendar Goud Badepally / Tales Rocha de Moura / Elżbieta Purta / Eugene F Baulin / Janusz M Bujnicki /
Abstract: Advancements in genome-wide sequence analysis have led to the discovery of numerous novel bacterial non-coding RNAs (ncRNAs). These ncRNAs have been categorized into various RNA families and classes ...Advancements in genome-wide sequence analysis have led to the discovery of numerous novel bacterial non-coding RNAs (ncRNAs). These ncRNAs have been categorized into various RNA families and classes based on their size, structure, function, and evolutionary relationships. One such ncRNA family, raiA, is notably abundant in the bacterial phyla Firmicutes and Actinobacteria and is remarkably well-conserved across many Gram-positive bacteria. In this study, we integrated cryo-electron microscopy single-particle analysis with computational modeling and biochemical techniques to elucidate the structural characteristics of raiA from Clostridium sp. CAG 138. Our findings reveal the globular 3D fold of raiA, providing valuable structural insights. This analysis paves the way for future investigations into the functional properties of raiA, potentially uncovering new regulatory mechanisms in bacterial ncRNAs.
History
DepositionJul 20, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51119.png

Downloads & links

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Map

FileDownload / File: emd_51119.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.18272607 - 0.46699923
Average (Standard dev.)0.00095649005 (±0.012733996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51119_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_51119_half_map_2.map
Projections & Slices
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Sample components

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Entire : raiA ncRNA

EntireName: raiA ncRNA
Components
  • Cell: raiA ncRNA
    • RNA: raiA (224-MER)

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Supramolecule #1: raiA ncRNA

SupramoleculeName: raiA ncRNA / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium sp. CAG:138 (bacteria)

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Macromolecule #1: raiA (224-MER)

MacromoleculeName: raiA (224-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Clostridium sp. CAG:138 (bacteria)
Molecular weightTheoretical: 72.829305 KDa
SequenceString: GGGAGUCGGG UCUGUGGUUG AAAGUCGAUG CCAGUCGCAG GCGAAACGAU CCACAUAAGC GGGGCAAAGU UCCCGUGAGC AUGGUGCGG CUUAGAUGUA AGUCCUGUCG UGCGGCAUUC CGAAUCGAAU GCGGUGCGAG AGUGGCAGUA GUGGGCGGCG U AAAGCUCA ...String:
GGGAGUCGGG UCUGUGGUUG AAAGUCGAUG CCAGUCGCAG GCGAAACGAU CCACAUAAGC GGGGCAAAGU UCCCGUGAGC AUGGUGCGG CUUAGAUGUA AGUCCUGUCG UGCGGCAUUC CGAAUCGAAU GCGGUGCGAG AGUGGCAGUA GUGGGCGGCG U AAAGCUCA GUAGCGAACC CACCGACAGG CGAGUGUGGG GGCAAAAACC AGGUCAGCCG ACUCCA

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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

Concentration1.9 mg/mL
BufferpH: 7.5
Details: 20 mM HEPES pH 7.5, 50 mM KCl, 50 mM NaCl, 1 mM MgCl2, 1 mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 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

Startup modelType of model: INSILICO MODEL / In silico model: Generated by BrickWorX
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 208685
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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