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- PDB-9zcb: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle... -

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Basic information

Entry
Database: PDB / ID: 9zcb
Title1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-1 dimer
Components1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle
KeywordsRNA / homodimer / 1-methyl-pseudouridine
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsMcRae, E.K.S. / Kumar, Y.D.
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 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle
B: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle


Theoretical massNumber of molelcules
Total (without water)475,4782
Polymers475,4782
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 twist corrected RNA origami 6-helix bundle


Mass: 237739.094 Da / Num. of mol.: 2 / 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: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 1-methyl-pseudouridine.
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.464 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Buffer solutionpH: 8 / Details: 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: In vitro transcribed with 1-methyl-pseudouridine triphosphate in place of UTP. Purified by size exclusion chromatography.
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 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)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7UCSF ChimeraXmodel fitting
8ISOLDEmodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8333 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Target criteria: geometry minimization
RefinementStereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1008.41 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001535118
ELECTRON MICROSCOPYf_angle_d0.440654896
ELECTRON MICROSCOPYf_chiral_restr0.02396944
ELECTRON MICROSCOPYf_plane_restr0.00331460
ELECTRON MICROSCOPYf_dihedral_angle_d22.087128346

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