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- EMDB-55635: The Traptamer with 2'-Fluoro-modified pyrimidines (FY RNA) -

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Basic information

Entry
Database: EMDB / ID: EMD-55635
TitleThe Traptamer with 2'-Fluoro-modified pyrimidines (FY RNA)
Map datacryo-EM map of 2-prime-fluoro-modified pyrimidine RNA origami structure; the Traptamer.
Sample
  • Complex: Single-stranded 3-helix tile origami devise with fluorescent aptamers Broccoli and Pepper made of 2'fluoro modified pyrimidine RNA
    • RNA: RNA (364-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: 9.9 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 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55635.png

Downloads & links

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Map

FileDownload / File: emd_55635.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA origami structure; the Traptamer.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 100 pix.
= 331.264 Å		3.31 Å/pix.
x 100 pix.
= 331.264 Å		3.31 Å/pix.
x 100 pix.
= 331.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.31264 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.78
Minimum - Maximum-0.2055146 - 1.7162833
Average (Standard dev.)0.0048510213 (±0.073137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 331.264 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 origami structure;...

Fileemd_55635_additional_1.map
Annotationcryo-EM map of 2-prime-fluoro-modified pyrimidine RNA origami structure; the Traptamer (sharp).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55635_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_55635_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 (364-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 (364-MER)

MacromoleculeName: RNA (364-MER) / type: rna / ID: 1
Source (natural)Organism: synthetic RNA (others)
SequenceString: GGAA(UFT)(CFZ)(UFT)(CFZ)G(CFZ) (CFZ)(CFZ)GA(UFT)G(UFT)(UFT)(CFZ)G (CFZ)A(UFT)(CFZ)GGGA(UFT)(UFT) (UFT)G(CFZ)AGG(UFT)(CFZ)(CFZ)A (UFT)GGA(UFT)(UFT)A(CFZ)A(CFZ) (CFZ)A(UFT)G(CFZ)AA(CFZ)G(CFZ) ...String:
GGAA(UFT)(CFZ)(UFT)(CFZ)G(CFZ) (CFZ)(CFZ)GA(UFT)G(UFT)(UFT)(CFZ)G (CFZ)A(UFT)(CFZ)GGGA(UFT)(UFT) (UFT)G(CFZ)AGG(UFT)(CFZ)(CFZ)A (UFT)GGA(UFT)(UFT)A(CFZ)A(CFZ) (CFZ)A(UFT)G(CFZ)AA(CFZ)G(CFZ) AGA(CFZ)(CFZ)(UFT)G(UFT)AG A(UFT)G(CFZ)(CFZ)A(CFZ)G(CFZ)(UFT) AG(CFZ)(CFZ)G(UFT)GG(UFT)G AGGG(UFT)(CFZ)GGG(UFT) (CFZ)(CFZ)AGA(UFT)G(UFT)(CFZ)A (UFT)(UFT)(CFZ)GA(CFZ)(UFT)(UFT)(UFT)A A(CFZ)G(CFZ)G(CFZ)(CFZ)(UFT)AA G(CFZ)G(UFT)(UFT)GAAGG (CFZ)G(UFT)G(UFT)(UFT)AGAG (CFZ)AGA(UFT)AG(UFT)(UFT)(CFZ) G(CFZ)(UFT)A(UFT)(CFZ)(UFT)GGG GAG(CFZ)(CFZ)(UFT)G(UFT)(UFT)(CFZ) G(CFZ)AGG(CFZ)(UFT)(CFZ)AG GAG(CFZ)(CFZ)(UFT)(UFT)(CFZ)GG G(CFZ)(UFT)(CFZ)(CFZ)(UFT)AG(CFZ)G (CFZ)(UFT)A(UFT)(UFT)A(CFZ)(CFZ)(CFZ)(CFZ) GGA(CFZ)A(CFZ)(CFZ)A(CFZ)(CFZ) GGG(CFZ)AGA(CFZ)AA G(UFT)AA(UFT)GG(UFT)G(CFZ) (UFT)(CFZ)(CFZ)(UFT)(CFZ)GAA(UFT)G A(CFZ)(UFT)(UFT)(CFZ)(UFT)G(UFT)(UFT)G AG(UFT)AGAG(UFT)G(UFT) GGG(CFZ)(UFT)(CFZ)(CFZ)G(CFZ)G G(CFZ)(UFT)AG(UFT)G(UFT)G(CFZ) A(CFZ)(CFZ)(UFT)(UFT)AG(CFZ)GG (UFT)GAA(UFT)G(UFT)(CFZ)(UFT)G A(CFZ)A(CFZ)(CFZ)G(UFT)(UFT)AA GG(UFT)GG(UFT)(UFT)A(CFZ)(UFT) (CFZ)(UFT)(UFT)(CFZ)GGAG(UFT)A A(CFZ)G(CFZ)(CFZ)GAGA(UFT) (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: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 107281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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