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9z1n

Structure of KP.3 spike in complex with Nanosota-9B (local refinement)

Method: ELECTRON MICROSCOPY D_max: 113.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z1n
deposition_date	2025-11-04
title	Structure of KP.3 spike in complex with Nanosota-9B (local refinement)
keywords	SARS-CoV-2, entry, 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	30.17 Å
rg_electron	30.63 Å
i0	32448200.00
molecular_weight	43891.0 kDa
excluded_volume	54695 Å³
envelope_volume	73658 Å³
shell_volume	23312 Å³
envelope_diameter	115.0 Å
shell_rg	32.55 Å
envelope_rg	31.23 Å
shape_rg	30.53 Å
total_rg	31.14 Å
total_atoms	3097
n_residues	395
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	113.6 Å
rg_real	30.75 Å
rg_real_error	1.34 Å
i0_real	3.2450e+07
i0_real_error	5.7340e+05
rg_reciprocal	30.50 Å
i0_reciprocal	32440000.0000
total_estimate	0.7128
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	23.6 Å
skewness	0.710
kurtosis	-0.128
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	9096000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.378; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.187; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	KP.3 spike
formula_weight	138311.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	3097

MFVFLVLLPLVSSQCVMPLFNLITTTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVFIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLESYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTKSNKKFLPFQQFGRDIVDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVSVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSRAGARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLFSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFLTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQLELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Source

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

Entity 2 polymer

description	Nanosota-9B
formula_weight	16304.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

QVQLQESGGGLVQPGGSLRLSCTASGIALHSKATGWFRQAPGKEREGVSCISSGDGTTYYEDSVEGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAADPSGVCHSGSYYYTDDDFYYRGQGTQVTVSSGGQHHHHHHGAYPYDVPDYAS

Source

organism	Vicugna pacos
common_name	alpaca
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

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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	3.440 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.44 Å
resolution_method	—
num_particles	95868

fit	/app/data/saxs_computation/z1/9z1n/9z1n.fit
pddf	/app/data/pr_computation/z1/9z1n/9z1n.pr.out
profile	/app/data/saxs_computation/z1/9z1n/9z1n.dat

Structure of KP.3 spike in complex with Nanosota-9B (local refinement)

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)