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- EMDB-55621: 2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the rec... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-55621
Title2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: PXT origami 'pointer')
Map dataFocus map of the FY RNA PXT with the anti-spike aptamer, from the data where it is in complex with the SARS-CoV-2 Spike protein.
Sample
  • Complex: Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptamer on a paranemic crossover triangle (PXT) and the SARS-CoV-2 Spike Protein
    • RNA: RNA
Keywordsorigami / modified nucleic acids / XNA / RNA / aptamer / 2'fluoro
Biological speciessynthetic construct (others) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.92 Å
AuthorsKristoffersen EL / Andersen ES / Zwergious NH
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Serum-stable RNA origami nano-devices
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_55621.png

Downloads & links

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Map

FileDownload / File: emd_55621.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus map of the FY RNA PXT with the anti-spike aptamer, from the data where it is in complex with the SARS-CoV-2 Spike protein.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 256 pix.
= 165.632 Å		0.65 Å/pix.
x 256 pix.
= 165.632 Å		0.65 Å/pix.
x 256 pix.
= 165.632 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.09271072 - 0.6713563
Average (Standard dev.)-0.00040471987 (±0.020136114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 165.632 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Focus map of the FY RNA PXT with...

Fileemd_55621_additional_1.map
AnnotationFocus map of the FY RNA PXT with the anti-spike aptamer, from the data where it is in complex with the SARS-CoV-2 Spike protein (sharp).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55621_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55621_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptam...

EntireName: Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptamer on a paranemic crossover triangle (PXT) and the SARS-CoV-2 Spike Protein
Components
  • Complex: Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptamer on a paranemic crossover triangle (PXT) and the SARS-CoV-2 Spike Protein
    • RNA: RNA

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Supramolecule #1: Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptam...

SupramoleculeName: Complex of 2'Fluoro modified pyrimidine (FY) RNA Anti-Spike aptamer on a paranemic crossover triangle (PXT) and the SARS-CoV-2 Spike Protein
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: FY RNA construct and protein were mixed at room temperature shortly before grid preparation.
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 650 KDa

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Macromolecule #1: RNA

MacromoleculeName: RNA / type: rna / ID: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
SequenceString: GGAAGG(UFT)GGG G(CFZ)A(CFZ)(UFT)(UFT)(CFZ)G(UFT)(UFT) (CFZ)G(CFZ)GAAG(UFT)G(CFZ) (CFZ)GG(CFZ)AAGA(UFT)(CFZ) (CFZ)(CFZ)(UFT)(CFZ)A(UFT)(CFZ)(UFT)(UFT)G (UFT)A(CFZ)G(UFT)(UFT)(CFZ)G(CFZ)G (UFT) ...String:
GGAAGG(UFT)GGG G(CFZ)A(CFZ)(UFT)(UFT)(CFZ)G(UFT)(UFT) (CFZ)G(CFZ)GAAG(UFT)G(CFZ) (CFZ)GG(CFZ)AAGA(UFT)(CFZ) (CFZ)(CFZ)(UFT)(CFZ)A(UFT)(CFZ)(UFT)(UFT)G (UFT)A(CFZ)G(UFT)(UFT)(CFZ)G(CFZ)G (UFT)G(CFZ)AAGA(CFZ)(CFZ)A (UFT)(CFZ)(CFZ)A(UFT)(CFZ)(UFT)(UFT)G(CFZ) (CFZ)(CFZ)AGG(CFZ)GA(CFZ)A (UFT)(UFT)(UFT)G(UFT)AA(UFT)(UFT)(CFZ) (CFZ)(UFT)GGA(CFZ)(CFZ)GA(UFT) A(CFZ)(UFT)(UFT)(CFZ)(CFZ)G(UFT)(CFZ)A GGA(CFZ)AGAGG(UFT) (UFT)G(CFZ)(CFZ)(UFT)G(CFZ)(CFZ)A(CFZ) (CFZ)(UFT)(UFT)(CFZ)(CFZ)A(CFZ)GA(CFZ) A(CFZ)GGAAAGGG (CFZ)(UFT)A(UFT)(UFT)(CFZ)G(UFT)AG (UFT)(CFZ)(CFZ)(UFT)(UFT)(UFT)(CFZ)(CFZ)(CFZ)(UFT) (UFT)(CFZ)G(UFT)(CFZ)AGGA(UFT) GGA(UFT)(CFZ)(UFT)A(CFZ)(CFZ)G G(UFT)G(UFT)(UFT)(CFZ)G(CFZ)A(UFT) (CFZ)GG(UFT)AGA(UFT)(UFT)G AGGG(UFT)GA(CFZ)GA AGAA(UFT)A(UFT)(CFZ)GG AGG(UFT)G(UFT)(UFT)(CFZ)G(CFZ) G(CFZ)(CFZ)(UFT)(UFT)(CFZ)GA(UFT)G (UFT)(UFT)G(UFT)G(UFT)(CFZ)G(UFT)

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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 mMPotasium ChloridKCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 109814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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