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- PDB-9zc9: 5-methyl-cytidine twist corrected RNA origami 6-helix bundle monomer -

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Basic information

Entry
Database: PDB / ID: 9zc9
Title5-methyl-cytidine twist corrected RNA origami 6-helix bundle monomer
Components5-methyl-cytidine twist corrected RNA origami 6-helix bundle
KeywordsRNA / 5-methyl-cytidine / modified base / homodimer
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 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 twist corrected RNA origami 6-helix bundle


Theoretical massNumber of molelcules
Total (without water)237,8511
Polymers237,8511
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 twist corrected RNA origami 6-helix bundle


Mass: 237851.219 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: Monomeric form of the m5C-6HBC-TC / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.235 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 8 / Details: 50mM HEPES pH 8.0, 50mM KCl, 5mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
14cryoSPARC3D reconstruction
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19587 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: geometry minimization
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDChain residue rangeDetailsInitial refinement model-IDPdb chain residue range
18id2

8id2

C8id2C11-14UUCG loop111-14
27PTl

7ptl

7PTlKissing loops2
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1191.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001517568
ELECTRON MICROSCOPYf_angle_d0.395927467
ELECTRON MICROSCOPYf_chiral_restr0.02293465
ELECTRON MICROSCOPYf_plane_restr0.0027730
ELECTRON MICROSCOPYf_dihedral_angle_d18.324813586

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