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9y5y

Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)

Method: ELECTRON MICROSCOPY D_max: 142.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y5y
deposition_date	2025-09-05
title	Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)
keywords	Inhibitor, Complex, Viral Spike Protein, Monobody, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN-VIRAL PROTEIN complex; ANTIVIRAL PROTEIN/VIRAL PROTEIN
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	44.68 Å
rg_electron	44.21 Å
i0	392873000.00
molecular_weight	167270.0 kDa
excluded_volume	210920 Å³
envelope_volume	302820 Å³
shell_volume	58171 Å³
envelope_diameter	144.9 Å
shell_rg	47.81 Å
envelope_rg	42.85 Å
shape_rg	44.20 Å
total_rg	44.45 Å
total_atoms	11824
n_residues	1490
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	142.0 Å
rg_real	44.65 Å
rg_real_error	1.02 Å
i0_real	3.9290e+08
i0_real_error	6.6640e+06
rg_reciprocal	44.68 Å
i0_reciprocal	392900000.0000
total_estimate	0.8223
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	56.8 Å
skewness	0.230
kurtosis	-0.540
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0001
highest_alpha	32800000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Spike protein S1
formula_weight	22195.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,C,E,G
atom_count	11824

NLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPK

Source

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

Entity 2 polymer

description	Monobody s19382
formula_weight	9858.2 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,I,J,K,L

TKLEVVAATPTSLLISWRMPMFTVDFYVIQYGETGGNSPVQVQVVPGSTRTATISGLKPGVDYTITVYAYVQRDNLHYPHPISINYRTG

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Homo sapiens

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	triclinic

resolution	3.16 Å
resolution_method	—
num_particles	230942

fit	/app/data/saxs_computation/y5/9y5y/9y5y.fit
pddf	/app/data/pr_computation/y5/9y5y/9y5y.pr.out
profile	/app/data/saxs_computation/y5/9y5y/9y5y.dat

Structure of the Omicron Spike RBD bound by the monobody s19382 (local refinement from dimerized Spike protein ECDs)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)