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- PDB-9zbr: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended ... -

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Basic information

Entry
Database: PDB / ID: 9zbr
Title1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation
Components1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme
KeywordsRNA / Tetrahymena ribozyme / m1Y / 1-methyl-pseudouridine / modified base
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsMcRae, E.K.S. / Yang, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230015 United States
CitationJournal: Nat Commun / Year: 2026
Title: Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.
Authors: Deepak Kumar Yadav / Haoyun Yang / Sukyeong Lee / Ewan K S McRae /
Abstract: Modified nucleotide bases like 5-methylcytosine (m5C) and N1-methyl-pseudouridine (m1Ψ) are widely used to enhance stability and reduce immunogenicity in therapeutic RNAs, yet their impact on RNA ...Modified nucleotide bases like 5-methylcytosine (m5C) and N1-methyl-pseudouridine (m1Ψ) are widely used to enhance stability and reduce immunogenicity in therapeutic RNAs, yet their impact on RNA tertiary structure remains unclear. Here we investigate how these modifications influence folding and function in both a synthetic RNA origami nanostructure and the natural Tetrahymena ribozyme. Using cryo-EM, FRET, and biochemical assays, we find that modified bases impede proper maturation of RNA origami by stabilizing alternative coaxial stacking at key junctions, leading to dimerization. In the ribozyme, modifications shift the equilibrium between open and closed conformations, altering catalytic activity in a temperature-dependent manner. These effects arise primarily from changes in base-stacking energetics rather than base pairing. Our findings reveal that base modifications reshape RNA folding landscapes and structure-function relationships, underscoring the need to consider structural consequences when designing modified RNAs for synthetic biology and therapeutic applications.
History
DepositionNov 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme


Theoretical massNumber of molelcules
Total (without water)126,4581
Polymers126,4581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme


Mass: 126457.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Tetrahymena thermophila (eukaryote) / References: GenBank: 10832
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.125 MDa / Experimental value: NO
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Buffer solutionpH: 8
Details: SEC purified in 50mM HEPES pH 8.0, 50mM KCl, 5mM MgCl2
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was transcribed in vitro with 1-methyl-pseudouridine triphosphate in place of UTP. Purified by size exclusion chromatography and refolded by heat denaturation and cooling to room ...Details: Sample was transcribed in vitro with 1-methyl-pseudouridine triphosphate in place of UTP. Purified by size exclusion chromatography and refolded by heat denaturation and cooling to room temperature prior to the addition of 10mM MgCl2
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategoryDetails (eV)
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Rosettamodel fittingDRRAFTER
10ISOLDEmodel refinement
11PHENIXmodel refinement
12Cootmodel refinement
13cryoSPARCinitial Euler assignment
14cryoSPARCfinal Euler assignment
15cryoSPARCclassification
16cryoSPARC3D reconstructionnon-uniform refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 599317 / Details: Blob picking on denoised micrographs
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 60417 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: geometry minimization
Atomic model buildingPDB-ID: 7XSN

7xsn


Accession code: 7XSN / Source name: PDB / Type: experimental model
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1557.1 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00139372
ELECTRON MICROSCOPYf_angle_d0.399914653
ELECTRON MICROSCOPYf_chiral_restr0.02181838
ELECTRON MICROSCOPYf_plane_restr0.0024387
ELECTRON MICROSCOPYf_dihedral_angle_d23.50787398

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