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- EMDB-55623: 2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-55623
Title2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (Full map, no symmetry)
Map dataMap of the SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain (no symetry imposed).
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
    • Protein or peptide: 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 / synthetic RNA (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_55623.png

Downloads & links

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Map

FileDownload / File: emd_55623.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain (no symetry imposed).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 640 pix.
= 621.12 Å		0.97 Å/pix.
x 640 pix.
= 621.12 Å		0.97 Å/pix.
x 640 pix.
= 621.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.2885185 - 0.75686055
Average (Standard dev.)-0.00025589968 (±0.009637425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 621.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Map of the SARS-CoV-2 Spike protein where a...

Fileemd_55623_additional_1.map
AnnotationMap of the SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain (no symetry imposed) (sharp).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55623_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 B

Fileemd_55623_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
    • Protein or peptide: 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: SARS-CoV-2 Spike protein

MacromoleculeName: SARS-CoV-2 Spike protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLGV YYHKNNKSWM ESEFRVYSSA NNCTFEYVSQ PFLMDLEGKQ ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNPV LPFNDGVYFA STEKSNIIRG WIFGTTLDSK TQSLLIVNNA TNVVIKVCEF QFCNDPFLGV YYHKNNKSWM ESEFRVYSSA NNCTFEYVSQ PFLMDLEGKQ GNFKNLREFV FKNIDGYFKI YSKHTPINLV RDLPQGFSAL EPLVDLPIGI NITRFQTLLA LHRSYLTPGD SSSGWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLCPFGEVFN ATRFASVYAW NRKRISNCVA DYSVLYNSAS FSTFKCYGVS PTKLNDLCFT NVYADSFVIR GDEVRQIAPG QTGKIADYNY KLPDDFTGCV IAWNSNNLDS KVGGNYNYLY RLFRKSNLKP FERDISTEIY QAGSTPCNGV EGFNCYFPLQ SYGFQPTNGV GYQPYRVVVL SFELLHAPAT VCGPKKSTNL VKNKCVNFNF NGLTGTGVLT ESNKKFLPFQ QFGRDIADTT DAVRDPQTLE ILDITPCSFG GVSVITPGTN TSNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCLIGA EHVNNSYECD IPIGAGICAS YQTQTNSPSG AGSVASQSII AYTMSLGAEN SVAYSNNSIA IPTNFTISVT TEILPVSMTK TSVDCTMYIC GDSTECSNLL LQYGSFCTQL NRALTGIAVE QDKNTQEVFA QVKQIYKTPP IKDFGGFNFS QILPDPSKPS KRSFIEDLLF NKVTLADAGF IKQYGDCLGD IAARDLICAQ KFNGLTVLPP LLTDEMIAQY TSALLAGTIT SGWTFGAGAA LQIPFAMQMA YRFNGIGVTQ NVLYENQKLI ANQFNSAIGK IQDSLSSTAS ALGKLQDVVN QNAQALNTLV KQLSSNFGAI SSVLNDILSR LDPPEAEVQI DRLITGRLQS LQTYVTQQLI RAAEIRASAN LAATKMSECV LGQSKRVDFC GKGYHLMSFP QSAPHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNTVYDPLQP ELDS

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2
Source (natural)Organism: synthetic RNA (others)
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 433417
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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