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9xgo

Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

Method: ELECTRON MICROSCOPY D_max: 110.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xgo
deposition_date	2025-10-30
title	Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain
keywords	;SARS-CoV-2; N-terminal domain; antibodies; N1/N2 loop; ACE2 competition, 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	31.85 Å
rg_electron	31.14 Å
i0	109537000.00
molecular_weight	83051.0 kDa
excluded_volume	103930 Å³
envelope_volume	137770 Å³
shell_volume	37430 Å³
envelope_diameter	117.1 Å
shell_rg	37.61 Å
envelope_rg	30.93 Å
shape_rg	31.09 Å
total_rg	31.89 Å
total_atoms	5859
n_residues	732
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	110.6 Å
rg_real	31.80 Å
rg_real_error	0.91 Å
i0_real	1.0950e+08
i0_real_error	1.8980e+06
rg_reciprocal	31.83 Å
i0_reciprocal	109500000.0000
total_estimate	0.8804
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.6 Å
skewness	0.264
kurtosis	-0.377
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	17460000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	BD58-0730 heavy chain
formula_weight	13364.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	5859

VQLVQSGAEVKKPGASVKVSCKASGYTFTSYYMHWVRQAPGQGLEWMGIINPSGGSTSNAQKFQGRVTMTRDTFTSTVYMELSSLRSEDTAVYYCARDIARGIGEYYFDYWGQGTLVTVSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	BD58-0730 light chain
formula_weight	11718.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QSALTQTASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQHPGKAPKLMIYDVYKRPSGVSNRFSGSKSGNTASLTISGLQAEDEADYYCSSYTTSSTLLFGGGTKLTVLGQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Spike protein S1
formula_weight	32433.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

CVNLITRTQSYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHAIHVSGTNGTKRFDNPALPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDVYQKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKEGNFKNLREFVFKNIDGYFKIYSKHTPINLERDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTL

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 4 polymer

description	Spike glycoprotein
formula_weight	25110.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

TESIVRFPNITNLCPFHEVFNATTFASVYAWNRKRISNCVADYSVIYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKPSGNYNYLYRLFRKSKLKPFERDISTEIYQAGNKPCNGVAGPNCYSPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNG

Source

organism	Severe acute respiratory syndrome coronavirus 2
common_name	2019-nCoV, SARS-CoV-2
ncbi_taxonomy_id	2697049
host_organism	Homo sapiens

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	7

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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	—

resolution	3.770 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.77 Å
resolution_method	—
num_particles	111000

fit	/app/data/saxs_computation/xg/9xgo/9xgo.fit
pddf	/app/data/pr_computation/xg/9xgo/9xgo.pr.out
profile	/app/data/saxs_computation/xg/9xgo/9xgo.dat

Omicron-specific ultra-potent SARS-CoV-2 neutralizing antibodies targeting the N1/N2 loop of Spike N-terminal domain

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

Refinement

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)