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- EMDB-45248: Group IIC intron embedded with the TPP riboswitch -

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Basic information

Entry
Database: EMDB / ID: EMD-45248
TitleGroup IIC intron embedded with the TPP riboswitch
Map data
Sample
  • Complex: Group IIC intron embedded with the TPP riboswitch
    • RNA: Group IIC intron embedded with the TPP riboswitch
  • Ligand: MAGNESIUM ION
KeywordsIntron / Splicing / Ribozyme / RNA
Biological speciesOceanobacillus iheyensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.41 Å
AuthorsToor N
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM141706 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122532 United States
CitationJournal: Nat Commun / Year: 2025
Title: Scaffold-enabled high-resolution cryo-EM structure determination of RNA.
Authors: Daniel B Haack / Boris Rudolfs / Shouhong Jin / Alexandra Khitun / 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. We demonstrate this technology by determining the structures of the 86-nucleotide (nt) thiamine pyrophosphate (TPP) riboswitch aptamer domain and the recently described 210-nt raiA bacterial non-coding RNA involved in sporulation and biofilm formation. In the case of the TPP riboswitch aptamer domain, the scaffolding approach allowed visualization of 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 adopts an open Y-shaped conformation in the absence of ligand. Using this scaffold approach, we determined the structure of raiA at 2.5 Å in the core. Our versatile scaffolding strategy enables efficient RNA structure determination for a broad range of small to moderate-sized RNAs, which were previously intractable for high-resolution cryo-EM studies.
History
DepositionJun 7, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45248.png

Downloads & links

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Map

FileDownload / File: emd_45248.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 400 pix.
= 324.4 Å		0.81 Å/pix.
x 400 pix.
= 324.4 Å		0.81 Å/pix.
x 400 pix.
= 324.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.811 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.34570268 - 1.0737231
Average (Standard dev.)0.00039552271 (±0.016491078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 324.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45248_additional_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_45248_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45248_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Group IIC intron embedded with the TPP riboswitch

EntireName: Group IIC intron embedded with the TPP riboswitch
Components
  • Complex: Group IIC intron embedded with the TPP riboswitch
    • RNA: Group IIC intron embedded with the TPP riboswitch
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Group IIC intron embedded with the TPP riboswitch

SupramoleculeName: Group IIC intron embedded with the TPP riboswitch / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Group IIC intron embedded with the TPP riboswitch

MacromoleculeName: Group IIC intron embedded with the TPP riboswitch / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 160.467078 KDa
SequenceString: GUUAUGUGUG CCCGGCAUGG GUGCAGUCUA UAGGGUGAGA GUCCCGAACU GUGAAGGCAG AAGUAACAGU UAGCCUAACG CAAGGGUGU CCGUGGCGAC AUGGAAUCUG AAGGAAGCGG ACGGCAAACC UUCGGUCUGA GGAACACGAA CUUCAUAUGA G GCUAGGUA ...String:
GUUAUGUGUG CCCGGCAUGG GUGCAGUCUA UAGGGUGAGA GUCCCGAACU GUGAAGGCAG AAGUAACAGU UAGCCUAACG CAAGGGUGU CCGUGGCGAC AUGGAAUCUG AAGGAAGCGG ACGGCAAACC UUCGGUCUGA GGAACACGAA CUUCAUAUGA G GCUAGGUA UCAAUGGAUG AGUUUGCAUA ACAAAACAAA GUCCUUUCUG CCAAAGUUGG UACAGAGUAA AUGAAGCAGA UU GAUGAAG GGAAAGACUG CAUUCUUACC CGGGGAGGUC UGGAAACAGA AGUCAGCAGA AGUCAUAGUA CCCUCAGUAC UCG GGGUGC CCUUCUGCGU GAAGGCUGAG AAAUACCCGU AUCACCUGAU CUGGAUAAUG CCAGCGUAGG GAAGUGCUGA GGGG AAGGA CGGAACAAGU AUGGCGUUCG CGCCUAAGCU UGAACCACCG UAUACCGAAC GGUACGUACG GUGGUGUGAG AGGAG UUCG CUCUACUCUA U

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 21 / 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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 655558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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