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9upr

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N103 and S2L20 Fab

Method: ELECTRON MICROSCOPY D_max: 121.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9upr
deposition_date	2025-04-28
title	Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N103 and S2L20 Fab
keywords	complex, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex, VIRAL 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	35.17 Å
rg_electron	35.03 Å
i0	113287000.00
molecular_weight	85218.0 kDa
excluded_volume	106680 Å³
envelope_volume	150130 Å³
shell_volume	38306 Å³
envelope_diameter	120.4 Å
shell_rg	38.76 Å
envelope_rg	35.00 Å
shape_rg	34.98 Å
total_rg	35.50 Å
total_atoms	6014
n_residues	763
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	121.2 Å
rg_real	35.41 Å
rg_real_error	1.25 Å
i0_real	1.1330e+08
i0_real_error	1.7310e+06
rg_reciprocal	35.26 Å
i0_reciprocal	113300000.0000
total_estimate	0.8506
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.7 Å
skewness	0.509
kurtosis	-0.331
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	16680000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.862

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	S2L20 light chain
formula_weight	26018.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6014

METDTLLLWVLLLWVPGSTGDVIWMTQSPSSLSASVGDRVTITCQASQDIRFYLNWYQQKPGKAPKLLISDASNMETGVPSRFSGSGSGTDFTFTISSLQPEDIATYYCQQYDNLPFTFGPGTKVDFKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECS

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	S2L20 heavy chain
formula_weight	52041.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

METDTLLLWVLLLWVPGSTGDEVQLVESGGGVVQPGGSLRLSCAASGFTFNSYGMHWVRQAPGKGLEWVAFIRYDGGNKYYADSVKGRFTISRDNSKNTLYLQMKSLRAEDTAVYYCANLKDSRYSGSYYDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	nanobody N103
formula_weight	12959.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

QVQLQESGGGLVQPGGSLRLSCAASVNLFIGATMAWYRQAPGNQRELVATIGAGGTTNYADSVKGRFTASRDDAKKTIYLQMNSLTPEDTAVYYCNYGSMSNPRTSGPNAFWGRGTQVTVSS

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Homo sapiens

Entity 4 polymer

description	Spike glycoprotein
formula_weight	34909.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHVISGTNGTKRFDNPVLPFNDGVYFASIEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVVIKVCEFQFCNDPFLDHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIREPEDLPQGFSALEPLVDLPIGINITRFQTLLALHRSYLTPGDSSSGWTAGAAAYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSHHHHHH

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 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 6 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	4

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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	2.770 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.77 Å
resolution_method	—
num_particles	185260

fit	/app/data/saxs_computation/up/9upr/9upr.fit
pddf	/app/data/pr_computation/up/9upr/9upr.pr.out
profile	/app/data/saxs_computation/up/9upr/9upr.dat

Cryo-EM structure of the N-terminal domain of Omicron BA.1 in complex with nanobody N103 and S2L20 Fab

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 branched

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)