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- PDB-9yn7: De Novo RNA Pseudocycle, pC2-240-0 -

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Basic information

Entry
Database: PDB / ID: 9yn7
TitleDe Novo RNA Pseudocycle, pC2-240-0
ComponentspC2-240-04: RNA (240-MER)
KeywordsRNA / De Novo RNA / RNA Pseudocycle / pC2-240-0
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.63 Å
Model detailsMODEL GENERATED BY ROSETTA VERSION 2025.37+release.df75a9c48e
AuthorsWeidle, C. / Favor, A.
Funding support United States, 4items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-043758 United States
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States)CHE-2226466 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NIGMS GM148166 United States
CitationJournal: To Be Published
Title: De novo design of RNA and nucleoprotein complexes
Authors: Favor, A. / Quijano, R. / Chernova, E. / Kubaney, A. / Weidle, C. / Esler, M.A. / McHugh, L. / Carr, A. / Hsia, Y. / Juergens, D. / Carr, K.D. / Kim, P.T. / Politanska, Y. / Sehgal, E. / ...Authors: Favor, A. / Quijano, R. / Chernova, E. / Kubaney, A. / Weidle, C. / Esler, M.A. / McHugh, L. / Carr, A. / Hsia, Y. / Juergens, D. / Carr, K.D. / Kim, P.T. / Politanska, Y. / Sehgal, E. / Kwon, P.S. / Pecoraro, R.J. / Glasscock, C. / Borst, A.J. / DiMaio, F. / Stoddard, B.L. / Baker, D.
History
DepositionOct 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 14, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pC2-240-04: RNA (240-MER)


Theoretical massNumber of molelcules
Total (without water)78,3911
Polymers78,3911
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 pC2-240-04: RNA (240-MER)


Mass: 78390.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: De Novo RNA Pseudocycle, pC2-240-0 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.07715999999999999 MDa / Experimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Buffer solutionpH: 8 / Details: 10 mM Magnesium Chloride,
Buffer componentConc.: 10 mM / Name: Magnesium Chloride / Formula: MgCl2
SpecimenConc.: 43 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 10 mM MgCl2
Specimen supportDetails: 15 eV / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5 sec. / Electron dose: 48.739 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 5 / Num. of real images: 8030
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 5482343 / Details: particles from template picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140174 / Algorithm: FOURIER SPACE / Details: Non Uniform Refinement / Num. of class averages: 1 / Symmetry type: POINT

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