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9t74

;2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer) ;

Method: ELECTRON MICROSCOPY D_max: 87.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t74
deposition_date	2025-11-10
title	;2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer) ;
keywords	;origami, modified nucleic acids, XNA, RNA, aptamer, 2'fluoro ;; RNA
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	24.25 Å
rg_electron	23.60 Å
i0	43183000.00
molecular_weight	39021.0 kDa
excluded_volume	43509 Å³
envelope_volume	58273 Å³
shell_volume	22147 Å³
envelope_diameter	96.4 Å
shell_rg	28.93 Å
envelope_rg	23.85 Å
shape_rg	23.47 Å
total_rg	24.39 Å
total_atoms	2673
n_residues	222
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	87.2 Å
rg_real	24.41 Å
rg_real_error	1.00 Å
i0_real	4.3180e+07
i0_real_error	7.3150e+05
rg_reciprocal	24.37 Å
i0_reciprocal	43180000.0000
total_estimate	0.7558
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	26.3 Å
skewness	0.546
kurtosis	0.029
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	3758000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.685; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.772; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA/RNA (51-MER)
formula_weight	16408.5 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	A
atom_count	2673

GGXGAXAUUUGUAAUUXXUGGAXXGAUAXUUXXGUXAGGAXAGAGGUUGXX

Source

organism	synthetic RNA
ncbi_taxonomy_id	2086595
host_organism	synthetic construct

Entity 2 polymer

description	Spike glycoprotein
formula_weight	125307.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPINLVRDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQDVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQTQTNSPSGAGSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLNRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKDFGGFNFSQILPDPSKPSKRSFIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGAALQIPFAMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTASALGKLQDVVNQNAQALNTLVKQLSSNFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDS

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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resolution	3.46 Å
resolution_method	—
num_particles	736847

fit	/app/data/saxs_computation/t7/9t74/9t74.fit
pddf	/app/data/pr_computation/t7/9t74/9t74.pr.out
profile	/app/data/saxs_computation/t7/9t74/9t74.dat

;2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer) ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)