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- PDB-9zc6: 5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme -

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Basic information

Entry
Database: PDB / ID: 9zc6
Title5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme
Components5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme
KeywordsRNA / Tetrahymena ribozyme / 5mC / 5-methyl-cytidine / 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: 4.9 Å
AuthorsMcRae, E.K.S.
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 22, 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: 5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme


Theoretical massNumber of molelcules
Total (without water)126,3991
Polymers126,3991
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain 5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme


Mass: 126398.992 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: 5mC-TR / 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: 50mM HEPES pH 8.0 , 10mM MgCl2
Buffer componentConc.: 50 mM / Name: HEPES-NA / Formula: HEPES-NA
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was transcribed in vitro with 5-methyl-cytidine triphosphate in place of CTP. Purified by size exclusion chromatography and refolded by heat denaturation and cooling to room ...Details: Sample was transcribed in vitro with 5-methyl-cytidine triphosphate in place of CTP. 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
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 25 K

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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 defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
8Rosettamodel fittingDRRAFTER
13cryoSPARC4.6.23D reconstruction
14ISOLDEmodel refinement
15PHENIXmodel refinement
17Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233268 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / 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: 333.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00149346
ELECTRON MICROSCOPYf_angle_d0.403614601
ELECTRON MICROSCOPYf_chiral_restr0.02161864
ELECTRON MICROSCOPYf_plane_restr0.0024387
ELECTRON MICROSCOPYf_dihedral_angle_d20.02716620

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