SAXSdb — 9z1m

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1. Structure Basics

entry_id	9z1m
deposition_date	2025-11-04
title	Cryo-EM structure of KP.3 spike in complex with Nb9B
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	56.94 Å
rg_electron	56.55 Å
i0	2338080000.00
molecular_weight	407800.0 kDa
excluded_volume	510880 Å³
envelope_volume	778760 Å³
shell_volume	116100 Å³
envelope_diameter	230.2 Å
shell_rg	58.53 Å
envelope_rg	55.66 Å
shape_rg	56.59 Å
total_rg	56.47 Å
total_atoms	28750
n_residues	3633
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	205.1 Å
rg_real	57.01 Å
rg_real_error	2.10 Å
i0_real	2.3380e+09
i0_real_error	4.5900e+07
rg_reciprocal	56.87 Å
i0_reciprocal	2338000000.0000
total_estimate	0.8474
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	65.9 Å
skewness	0.451
kurtosis	0.034
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0000
highest_alpha	262700000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.861

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Nanosota-9B
formula_weight	16304.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	D,E,F
atom_count	28750

QVQLQESGGGLVQPGGSLRLSCTASGIALHSKATGWFRQAPGKEREGVSCISSGDGTTYYEDSVEGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAADPSGVCHSGSYYYTDDDFYYRGQGTQVTVSSGGQHHHHHHGAYPYDVPDYAS

Source

organism	Vicugna pacos
common_name	alpaca
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polypeptide(L)
strand_id	B,C,A

MFVFLVLLPLVSSQCVMPLFNLITTTQSYTNSFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNVFIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIGRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFAPFFAFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLESYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTKSNKKFLPFQQFGRDIVDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVSVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGICASYQTQTKSRAGARSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLFSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFLTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQLELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIKGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGHHHHHH

Source

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

Entity 3 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	11

Entity 4 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	3.060 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.06 Å
resolution_method	—
num_particles	95868

fit	/app/data/saxs_computation/z1/9z1m/9z1m.fit
pddf	/app/data/pr_computation/z1/9z1m/9z1m.pr.out
profile	/app/data/saxs_computation/z1/9z1m/9z1m.dat

Cryo-EM structure of KP.3 spike in complex with Nb9B

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)