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- EMDB-55626: 3-helix origami tile + Broccoli and Pepper aptamers (3HT-BP) with... -

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Basic information

Entry
Database: EMDB / ID: EMD-55626
Title3-helix origami tile + Broccoli and Pepper aptamers (3HT-BP) with 2'-Fluoro-modified pyrimidines (FY RNA)
Map datacryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 3-helix tile origami structure with Broccoli and Pepper (3HT-BP).
Sample
  • Complex: Single-stranded 3-helix tile origami devise with fluorescent aptamers Broccoli and Pepper made of 2'fluoro modified pyrimidine RNA
    • RNA: RNA (375-MER)
Keywordsorigami / modified nucleic acids / XNA / RNA / crossover / tetra-loop / 2'fluoro
Biological speciessynthetic construct (others) / synthetic RNA (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.41 Å
AuthorsKristoffersen EL / Andersen ES / Zwergius NH
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Serum-stable RNA origami nanodevices
Authors: Kristoffersen EL / Zwergius NH / Vallina NS / Gluck N / Stange A / Desdorf L / Civit L / Geary C / Kjems J / Valero J / Andersen ES
History
DepositionNov 10, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55626.png

Downloads & links

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Map

FileDownload / File: emd_55626.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 3-helix tile origami structure with Broccoli and Pepper (3HT-BP).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.52 Å/pix.
x 256 pix.
= 388.096 Å		1.52 Å/pix.
x 256 pix.
= 388.096 Å		1.52 Å/pix.
x 256 pix.
= 388.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.516 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.12866558 - 0.74187106
Average (Standard dev.)0.00004188273 (±0.017676044)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 388.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: cryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 3-helix tile...

Fileemd_55626_additional_1.map
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA 3-helix tile origami structure with Broccoli and Pepper (3HT-BP) (sharp).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55626_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55626_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Single-stranded 3-helix tile origami devise with fluorescent apta...

EntireName: Single-stranded 3-helix tile origami devise with fluorescent aptamers Broccoli and Pepper made of 2'fluoro modified pyrimidine RNA
Components
  • Complex: Single-stranded 3-helix tile origami devise with fluorescent aptamers Broccoli and Pepper made of 2'fluoro modified pyrimidine RNA
    • RNA: RNA (375-MER)

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Supramolecule #1: Single-stranded 3-helix tile origami devise with fluorescent apta...

SupramoleculeName: Single-stranded 3-helix tile origami devise with fluorescent aptamers Broccoli and Pepper made of 2'fluoro modified pyrimidine RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: In vitro transcribed using mutant (Y639F) T7 RNA polymerase. Imaged in the presence of molecular dyes HBC620 and DFHBI-1T (see publication for additional details)
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: RNA (375-MER)

MacromoleculeName: RNA (375-MER) / type: rna / ID: 1
Source (natural)Organism: synthetic RNA (others)
SequenceString: GGA(UFT)A(CFZ)G(UFT)(CFZ)(UFT) A(CFZ)G(CFZ)(UFT)(CFZ)AG(UFT)G A(CFZ)GGA(CFZ)(UFT)(CFZ)(UFT)(CFZ) (UFT)(UFT)(CFZ)GGAGAG(UFT) (CFZ)(UFT)GA(CFZ)A(UFT)(CFZ)(CFZ)G AA(CFZ)(CFZ)A(UFT)A(CFZ)A(CFZ) ...String:
GGA(UFT)A(CFZ)G(UFT)(CFZ)(UFT) A(CFZ)G(CFZ)(UFT)(CFZ)AG(UFT)G A(CFZ)GGA(CFZ)(UFT)(CFZ)(UFT)(CFZ) (UFT)(UFT)(CFZ)GGAGAG(UFT) (CFZ)(UFT)GA(CFZ)A(UFT)(CFZ)(CFZ)G AA(CFZ)(CFZ)A(UFT)A(CFZ)A(CFZ) GGA(UFT)G(UFT)G(CFZ)(CFZ)(UFT) (CFZ)G(CFZ)(CFZ)GAA(CFZ)AG (UFT)(CFZ)(UFT)A(CFZ)GG(CFZ)GA G(CFZ)(UFT)(UFT)AAG(CFZ)G(CFZ) (UFT)GGGGA(CFZ)G(CFZ)(CFZ) (CFZ)AA(CFZ)G(CFZ)A(UFT)(CFZ)A (CFZ)AAAGA(CFZ)(UFT)GA G(UFT)GA(UFT)GAA(CFZ)(CFZ) AGAAG(UFT)A(UFT)GG A(CFZ)(UFT)GG(UFT)(UFT)G(CFZ)G (UFT)(UFT)GG(UFT)GGAGA (CFZ)GG(UFT)(CFZ)GGG(UFT)(CFZ) (CFZ)AG(UFT)(UFT)(CFZ)G(CFZ)(UFT)G (UFT)(CFZ)GAG(UFT)AGAG (UFT)G(UFT)GGG(CFZ)(UFT)(CFZ)(CFZ) A(UFT)(CFZ)GA(CFZ)G(CFZ)(CFZ)G (CFZ)(UFT)(UFT)(UFT)AAGG(UFT)(CFZ) (CFZ)(CFZ)(CFZ)AA(UFT)(CFZ)G(UFT)G G(CFZ)G(UFT)G(UFT)(CFZ)GG(CFZ) (CFZ)(UFT)G(CFZ)(UFT)(UFT)(CFZ)GG(CFZ) AGG(CFZ)A(CFZ)(UFT)GG(CFZ) G(CFZ)(CFZ)GGGA(CFZ)(CFZ)(UFT) (UFT)GAAGAGA(UFT)G AGA(UFT)(UFT)(UFT)(CFZ)GA(UFT) (CFZ)(UFT)(CFZ)A(UFT)(CFZ)(UFT)(UFT)(UFT)G GG(UFT)G(UFT)(CFZ)(UFT)(CFZ)(UFT)G G(UFT)G(CFZ)(UFT)(UFT)GAGG G(CFZ)(CFZ)(CFZ)(UFT)G(UFT)G(UFT)(UFT) (CFZ)G(CFZ)A(CFZ)AGGG(CFZ) (CFZ)G(CFZ)(UFT)(CFZ)A(CFZ)(UFT)GG G(UFT)G(UFT)GGA(CFZ)G(UFT) A(UFT)(CFZ)(CFZ)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationNameFormula
40.0 mMHEPES
5.0 mMMagnesium ChlorideMgCl2
50.0 mMPotassium ChlorideKCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 4449 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 11486
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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