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- EMDB-45247: Cryo-EM structure of a group IIC intron RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-45247
TitleCryo-EM structure of a group IIC intron RNA
Map data
Sample
  • Complex: Group IIC Intron
    • RNA: Group IIC Intron
  • Ligand: MAGNESIUM ION
Keywordssplicing / ribozyme / RNA
Biological speciesOceanobacillus iheyensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.56 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-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45247.png

Downloads & links

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Map

FileDownload / File: emd_45247.map.gz / Format: CCP4 / Size: 52.7 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.)
1.22 Å/pix.
x 240 pix.
= 292.08 Å		1.22 Å/pix.
x 240 pix.
= 292.08 Å		1.22 Å/pix.
x 240 pix.
= 292.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.217 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-0.7777769 - 2.6760447
Average (Standard dev.)0.00072626706 (±0.058366198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 292.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45247_additional_1.map
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Half map: #2

Fileemd_45247_half_map_1.map
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Half map: #1

Fileemd_45247_half_map_2.map
Projections & Slices
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Sample components

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Entire : Group IIC Intron

EntireName: Group IIC Intron
Components
  • Complex: Group IIC Intron
    • RNA: Group IIC Intron
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Group IIC Intron

SupramoleculeName: Group IIC Intron / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 135 KDa

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Macromolecule #1: Group IIC Intron

MacromoleculeName: Group IIC Intron / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 135.229062 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 CCCUGUUCGC AGG GGAAGG ACGGAACAAG UAUGGCGUUC GCGCCUAAGC UUGAACCACC GUAUACCGAA CGGUACGUAC GGUGGUGUGA GAGG AGUUC GCUCUACUCU AU

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 382753
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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