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- EMDB-48540: CryoEM Structure of the Candida albicans Group I Intron-Compound ... -

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Basic information

Entry
Database: EMDB / ID: EMD-48540
TitleCryoEM Structure of the Candida albicans Group I Intron-Compound 11 Complex under Calcium Condition
Map data
Sample
  • Complex: Complex of group I intron with small molecule Ca
    • RNA: RNA (332-MER)
  • Ligand: N~4~-(2-aminoethyl)-N~4~-methylpyrimidine-2,4-diamine
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsIntron / Group I / Splicing / RNA
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsChung K / Xu L / Liu T / Pyle A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Molecular insights into de novo small-molecule recognition by an intron RNA structure.
Authors: Tianshuo Liu / Ling Xu / Kevin Chung / Luke J Sisto / Jimin Hwang / Chengxin Zhang / Michael C Van Zandt / Anna Marie Pyle /
Abstract: Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the ...Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.
History
DepositionJan 6, 2025-
Header (metadata) releaseApr 30, 2025-
Map releaseApr 30, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48540.png

Downloads & links

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Map

FileDownload / File: emd_48540.map.gz / Format: CCP4 / Size: 125 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.)
0.74 Å/pix.
x 320 pix.
= 237.76 Å		0.74 Å/pix.
x 320 pix.
= 237.76 Å		0.74 Å/pix.
x 320 pix.
= 237.76 Å

Surface

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Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.743 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-2.1481907 - 3.1415803
Average (Standard dev.)-0.0004745688 (±0.036303084)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 237.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48540_msk_1.map
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Additional map: #1

Fileemd_48540_additional_1.map
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Half map: #2

Fileemd_48540_half_map_1.map
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Half map: #1

Fileemd_48540_half_map_2.map
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Sample components

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Entire : Complex of group I intron with small molecule Ca

EntireName: Complex of group I intron with small molecule Ca
Components
  • Complex: Complex of group I intron with small molecule Ca
    • RNA: RNA (332-MER)
  • Ligand: N~4~-(2-aminoethyl)-N~4~-methylpyrimidine-2,4-diamine
  • Ligand: POTASSIUM ION
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Complex of group I intron with small molecule Ca

SupramoleculeName: Complex of group I intron with small molecule Ca / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Candida albicans (yeast)

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Macromolecule #1: RNA (332-MER)

MacromoleculeName: RNA (332-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 106.727062 KDa
SequenceString: CGCUAGGGAU AAACUGUUUG UCCCUUUAUA UAGAGAUAUA UAGAAUAACA AUCGGGUGAA UUGCAAGAAU ACCACCCACC UCCUUUGGA GGUGGGUGAC AAUUUGCAGC GAAGUAUAUA UUAGCUUAAU AAUAAAAUAU UAUUUAGAUA UAUAAACGUU C AACGACUA ...String:
CGCUAGGGAU AAACUGUUUG UCCCUUUAUA UAGAGAUAUA UAGAAUAACA AUCGGGUGAA UUGCAAGAAU ACCACCCACC UCCUUUGGA GGUGGGUGAC AAUUUGCAGC GAAGUAUAUA UUAGCUUAAU AAUAAAAUAU UAUUUAGAUA UAUAAACGUU C AACGACUA GAAGGUGAGU AAGCUAACAA UAACCCUUCC ACGAGCGCCC GACAUCUUAA UGAACCAACA AUUACAAUUA AU UAAAGGU CAUUAUGAUG AUGACAUAGU CUGAACUAAA UAGUGAUAUU UAGAUAUAAU AUUUAAAUGA UAUUAUGAUA ACA AAAUUG AACAGG

GENBANK: GENBANK: NC_018046.1

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Macromolecule #2: N~4~-(2-aminoethyl)-N~4~-methylpyrimidine-2,4-diamine

MacromoleculeName: N~4~-(2-aminoethyl)-N~4~-methylpyrimidine-2,4-diamine / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1BNU
Molecular weightTheoretical: 167.212 Da

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 26 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5 / Details: 50 mM K-HEPES pH 7.5 and 10 mM CaCl2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 0.5 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: PDB ENTRY
PDB model - PDB ID:

1y0q

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 316599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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