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- EMDB-55622: 2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-55622
Title2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: Spike core)
Map dataFocus map of the core of SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain.
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
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: 2.78 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_55622.png

Downloads & links

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Map

FileDownload / File: emd_55622.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus map of the core of SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain.
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: 0.1
Minimum - Maximum-0.4960242 - 0.83728206
Average (Standard dev.)0.00003958112 (±0.0075512766)
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: Focus map of the core of SARS-CoV-2 Spike...

Fileemd_55622_additional_1.map
AnnotationFocus map of the core of SARS-CoV-2 Spike protein where a FY RNA anti-spike aptamer is bound to the RBD domain (sharp).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55622_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_55622_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

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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 NGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE F QFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG ...String:
QCVNLTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFDNP VLPFNDGVYF ASTEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE F QFCNDPFL GVYYHKNNKS WMESEFRVYS SANNCTFEYV SQPFLMDLEG KQGNFKNLRE FV FKNIDGY FKIYSKHTPI NLVRDLPQGF SALEPLVDLP IGINITRFQT LLALHRSYLT PGD SSSGWT AGAAAYYVGY LQPRTFLLKY NENGTITDAV DCALDPLSET KCTLKSFTVE KGIY QTSNF RVQPTESIVR FPNITNLCPF GEVFNATRFA SVYAWNRKRI SNCVADYSVL YNSAS FSTF KCYGVSPTKL NDLCFTNVYA DSFVIRGDEV RQIAPGQTGK IADYNYKLPD DFTGCV IAW NSNNLDSKVG GNYNYLYRLF RKSNLKPFER DISTEIYQAG STPCNGVEGF NCYFPLQ SY GFQPTNGVGY QPYRVVVLSF ELLHAPATVC GPKKSTNLVK NKCVNFNFNG LTGTGVLT E SNKKFLPFQQ FGRDIADTTD AVRDPQTLEI LDITPCSFGG VSVITPGTNT SNQVAVLYQ DVNCTEVPVA IHADQLTPTW RVYSTGSNVF QTRAGCLIGA EHVNNSYECD IPIGAGICAS YQTQTNSPS GAGSVASQSI IAYTMSLGAE NSVAYSNNSI AIPTNFTISV TTEILPVSMT K TSVDCTMY ICGDSTECSN LLLQYGSFCT QLNRALTGIA VEQDKNTQEV FAQVKQIYKT PP IKDFGGF NFSQILPDPS KPSKRSFIED LLFNKVTLAD AGFIKQYGDC LGDIAARDLI CAQ KFNGLT VLPPLLTDEM IAQYTSALLA GTITSGWTFG AGAALQIPFA MQMAYRFNGI GVTQ NVLYE NQKLIANQFN SAIGKIQDSL SSTASALGKL QDVVNQNAQA LNTLVKQLSS NFGAI SSVL NDILSRLDPP EAEVQIDRLI TGRLQSLQTY VTQQLIRAAE IRASANLAAT KMSECV LGQ SKRVDFCGKG YHLMSFPQSA PHGVVFLHVT YVPAQEKNFT TAPAICHDGK AHFPREG VF VSNGTHWFVT QRNFYEPQII TTDNTFVSGN CDVVIGIVNN TVYDPLQPEL DS

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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: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1300251
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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