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11oo

SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 germline Fab and LC-Kappa VHH

Method: ELECTRON MICROSCOPY D_max: 117.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11oo
deposition_date	2026-03-06
title	SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 germline Fab and LC-Kappa VHH
keywords	germline, antibody, rbd, omicron, ba.4, IMMUNE SYSTEM, IMMUNE SYSTEM-Viral Protein complex; IMMUNE SYSTEM/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	33.70 Å
rg_electron	33.60 Å
i0	108726000.00
molecular_weight	81794.0 kDa
excluded_volume	101690 Å³
envelope_volume	133950 Å³
shell_volume	35496 Å³
envelope_diameter	117.9 Å
shell_rg	37.89 Å
envelope_rg	33.52 Å
shape_rg	33.56 Å
total_rg	34.08 Å
total_atoms	5767
n_residues	746
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	117.2 Å
rg_real	33.89 Å
rg_real_error	1.20 Å
i0_real	1.0870e+08
i0_real_error	1.9610e+06
rg_reciprocal	33.77 Å
i0_reciprocal	108700000.0000
total_estimate	0.6668
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.9 Å
skewness	0.504
kurtosis	-0.254
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	15030000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 0.214; Positv: 1.000; Valcen: 0.779; Smooth: 0.843

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Omi32 germline light chain
formula_weight	23460.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L
atom_count	5778

EIVLTQSPGTLSLSPGERATLSCRASQSVSSSYLAWYQQKPGQAPRLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGSSPRLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	SARS-CoV-2 Omicron BA.4 spike protein
formula_weight	22315.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

HHTNLCPFDEVFNATRFASVYAWNRKRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIRGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKVGGNYNYRYRLFRKSNLKPFERDISTEIYQAGNKPCNGVAGVNCYFPLQSYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	LC-Kappa VHH
formula_weight	13162.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

EVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVATARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Saccharomyces cerevisiae

Entity 4 polymer

description	Omi32 germline heavy chain
formula_weight	23379.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVIWYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARDTAPPDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
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	1

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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	3.40 Å
resolution_method	—
num_particles	160551

fit	/app/data/saxs_computation/1o/11oo/11oo.fit
pddf	/app/data/pr_computation/1o/11oo/11oo.pr.out
profile	/app/data/saxs_computation/1o/11oo/11oo.dat

SARS-CoV-2 Omicron BA.4 RBD in complex with Omi32 germline Fab and LC-Kappa VHH

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 (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)