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- PDB-9sd9: 6-Helix Bundle - with a Clasp (6HB-C)-dimer with 2'-Fluoro-modifi... -

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Basic information

Entry
Database: PDB / ID: 9sd9
Title6-Helix Bundle - with a Clasp (6HB-C)-dimer with 2'-Fluoro-modified pyrimidines (FY RNA)
ComponentsRNA (720-MER)
KeywordsRNA / origami / modified nucleic acids / XNA / crossover / tetra-loop / kissing-loop / homo-dimer / 2'fluoro
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic RNA (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsKristoffersen, E.L. / Andersen, E.S. / Zwergius, N.H.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Serum-stable RNA origami nanodevices
Authors: Kristoffersen, E.L. / Zwergius, N.H. / Vallina, N.S. / Gluck, N. / Stange, A. / Desdorf, L. / Civit, L. / Geary, C. / Kjems, J. / Valero, J. / Andersen, E.S.
History
DepositionAug 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (720-MER)
B: RNA (720-MER)


Theoretical massNumber of molelcules
Total (without water)465,3362
Polymers465,3362
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 RNA (720-MER)


Mass: 232667.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic RNA (others)
Has ligand of interestY
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: Single-stranded 6HB-C-dimer made of 2'fluoro modified pyrimidine RNA
Type: COMPLEX
Details: In vitro transcribed using mutant (Y639F) T7 RNA polymerase
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
140 mMHEPES1
25 mMMagnesium ChlorideMgCl21
350 mMPotassium ChlorideKCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 278 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: 130000 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: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4449
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49938 / Symmetry type: POINT

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