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9uxs

The local refine of 3D reconstruction of the complex formed by SARS-CoV2 BA.1 spike glycoprotein and a single-domain antibody

Method: ELECTRON MICROSCOPY D_max: 71.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uxs
deposition_date	2025-05-14
title	The local refine of 3D reconstruction of the complex formed by SARS-CoV2 BA.1 spike glycoprotein and a single-domain antibody
keywords	SARS-CoV2, RBD, Single-domain antibody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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	22.49 Å
rg_electron	21.53 Å
i0	22105700.00
molecular_weight	36211.0 kDa
excluded_volume	45446 Å³
envelope_volume	55852 Å³
shell_volume	22045 Å³
envelope_diameter	73.1 Å
shell_rg	27.86 Å
envelope_rg	21.81 Å
shape_rg	21.49 Å
total_rg	22.52 Å
total_atoms	2559
n_residues	316
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	71.9 Å
rg_real	22.43 Å
rg_real_error	0.46 Å
i0_real	2.2110e+07
i0_real_error	2.9700e+05
rg_reciprocal	22.45 Å
i0_reciprocal	22110000.0000
total_estimate	0.9043
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	27.2 Å
skewness	0.224
kurtosis	-0.480
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	4417000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.963

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	single-domain antibody
formula_weight	15896.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2559

PSVLCLPPKPKDTLMISRTPEVTCVVSDYNPHHIYKFKWYVDGVEVHNAQTKPREEYDYLNARVVDKLTVLHQDWLNGKEYKCKVSASDEYYYDSRGYYRGASDIWGPIECTISKAKGQAGHHHHHHGDYKDDDDKG

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Spike glycoprotein
formula_weight	138088.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIVREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNITNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNLAPFFTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVSGNYNYLYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGFNCYFPLRSYSFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLKGTGVLTESNKKFLPFQQFGRDIADTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSRSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFKGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLSSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQPELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGRSLEVLFQGPGGGGGSGGGGSHHHHHH

Source

organism	Severe acute respiratory syndrome coronavirus 2
ncbi_taxonomy_id	2697049
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	3.40 Å
resolution_method	—
num_particles	204934

fit	/app/data/saxs_computation/ux/9uxs/9uxs.fit
pddf	/app/data/pr_computation/ux/9uxs/9uxs.pr.out
profile	/app/data/saxs_computation/ux/9uxs/9uxs.dat

The local refine of 3D reconstruction of the complex formed by SARS-CoV2 BA.1 spike glycoprotein and a single-domain antibody

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)