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- EMDB-45988: Cryo-EM structure of the Rail RNA motif -

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Basic information

Entry
Database: EMDB / ID: EMD-45988
TitleCryo-EM structure of the Rail RNA motif
Map data
Sample
  • Organelle or cellular component: Bacterial RaiA RNA motif
    • RNA: RNA (200-MER)
  • Ligand: MAGNESIUM ION
Keywordsnon-coding RNA / cryo-EM / structural biology / RNA
Biological speciesClostridium acetobutylicum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsRudolfs B / Haack DB / Toor N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141706 United States
CitationJournal: bioRxiv / Year: 2024
Title: Scaffold-enabled high-resolution cryo-EM structure determination of RNA.
Authors: Daniel B Haack / Boris Rudolfs / Shouhong Jin / Kevin M Weeks / Navtej Toor /
Abstract: Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are ...Cryo-EM structure determination of protein-free RNAs has remained difficult with most attempts yielding low to moderate resolution and lacking nucleotide-level detail. These difficulties are compounded for small RNAs as cryo-EM is inherently more difficult for lower molecular weight macromolecules. Here we present a strategy for fusing small RNAs to a group II intron that yields high resolution structures of the appended RNA, which we demonstrate with the 86-nucleotide thiamine pyrophosphate (TPP) riboswitch, and visualizing the riboswitch ligand binding pocket at 2.5 Å resolution. We also determined the structure of the ligand-free apo state and observe that the aptamer domain of the riboswitch undergoes a large-scale conformational change upon ligand binding, illustrating how small molecule binding to an RNA can induce large effects on gene expression. This study both sets a new standard for cryo-EM riboswitch visualization and offers a versatile strategy applicable to a broad range of small to moderate-sized RNAs, which were previously intractable for high-resolution cryo-EM studies.
History
DepositionJul 31, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45988.png

Downloads & links

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Map

FileDownload / File: emd_45988.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 325.632 Å		0.85 Å/pix.
x 384 pix.
= 325.632 Å		0.85 Å/pix.
x 384 pix.
= 325.632 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.848 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.2125182 - 0.66790056
Average (Standard dev.)-0.000113026384 (±0.008755612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 325.632 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Map

Fileemd_45988_additional_1.map
AnnotationSharpened Map
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Half map: #1

Fileemd_45988_half_map_1.map
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Half map: #2

Fileemd_45988_half_map_2.map
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Sample components

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Entire : Bacterial RaiA RNA motif

EntireName: Bacterial RaiA RNA motif
Components
  • Organelle or cellular component: Bacterial RaiA RNA motif
    • RNA: RNA (200-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Bacterial RaiA RNA motif

SupramoleculeName: Bacterial RaiA RNA motif / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridium acetobutylicum (bacteria) / Synthetically produced: Yes

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Macromolecule #1: RNA (200-MER)

MacromoleculeName: RNA (200-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Clostridium acetobutylicum (bacteria)
Molecular weightTheoretical: 192.022938 KDa
SequenceString: GUGUGCCCGG CAUGGGUGCA GUCUAUAGGG UGAGAGUCCC GAACUGUGAA GGCAGAAGUA ACAGUUAGCC UAACGCAAGG GUGUCCGUG GCGACAUGGA AUCUGAAGGA AGCGGACGGC AAACCUUCGG UCUGAGGAAC ACGAACUUCA UAUGAGGCUA G GUAUCAAU ...String:
GUGUGCCCGG CAUGGGUGCA GUCUAUAGGG UGAGAGUCCC GAACUGUGAA GGCAGAAGUA ACAGUUAGCC UAACGCAAGG GUGUCCGUG GCGACAUGGA AUCUGAAGGA AGCGGACGGC AAACCUUCGG UCUGAGGAAC ACGAACUUCA UAUGAGGCUA G GUAUCAAU GGAUGAGUUU GCAUAACAAA ACAAAGUCCU UUCUGCCAAA GUUGGUACAG AGUAAAUGAA GCAGAUUGAU GA AGGGAAA GACUGCAUUC UUACCCGGGG AGGUCUGAGC UUUCGAGCUC AGAAGUCAGC AGAAGUCAUA GUACCCUUAA GUU AGGUUU GUGGUUGAAA GUCGAUGCCA GUCGCAGGCA AAACGAUCCA CGUAAGUUAA ACAAAGUUUU AAUGAGCAUG GUGC GGCUU AGAAGUAAGU CCUGCCGCUU UAGGCGAGAG UAUUAGUAGU GAGAGGGUAA UUCCGGGUAG CGAAACUUCC AGCAG GCGA GUGUGGGGUC AAAGACCAGG UCAACUAACU UAAGGGGAAG GACGGAACAA GUAUGGCGUU CGCGCCAUGC UUGAAC CAC CGUAUACCGA ACGGUACGUA CGGUGGUGU

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 22 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 6.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 308340
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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