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- PDB-9zbq: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme -

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Basic information

Entry
Database: PDB / ID: 9zbq
Title1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme
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: 5.3 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: To Be Published
Title: Base modifications reshape RNA folding landscapes and structure function relationships in synthetic and natural RNAs
Authors: Kumar, D.Y. / Yang, H. / Lee, S. / McRae, E.K.S.
History
DepositionNov 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,7641
Polymers126,7641
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: 126763.758 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
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Rosettamodel fittingDRRAFTER
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstructionnon-uniform refinement
14ISOLDEmodel refinement
15PHENIXmodel refinement
16Cootmodel 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: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154365 / 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: 342.92 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00129372
ELECTRON MICROSCOPYf_angle_d0.383214653
ELECTRON MICROSCOPYf_chiral_restr0.01991837
ELECTRON MICROSCOPYf_plane_restr0.0022387
ELECTRON MICROSCOPYf_dihedral_angle_d22.55757397

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