Local refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein

Method: ELECTRON MICROSCOPY D_max: 121.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uel
deposition_date	2025-04-08
title	Local refinement of NTD and RBD domains of SARS-CoV2 KP.3.1.1 spike protein
keywords	Spike glycoprotein, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	36.86 Å
rg_electron	36.07 Å
i0	62809600.00
molecular_weight	63533.0 kDa
excluded_volume	79488 Å³
envelope_volume	120910 Å³
shell_volume	28456 Å³
envelope_diameter	121.4 Å
shell_rg	41.92 Å
envelope_rg	34.86 Å
shape_rg	36.07 Å
total_rg	36.54 Å
total_atoms	4485
n_residues	576
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

▼

3. P(r) Analysis (GNOM)

dmax	121.8 Å
rg_real	36.94 Å
rg_real_error	1.37 Å
i0_real	6.2810e+07
i0_real_error	1.2010e+06
rg_reciprocal	36.90 Å
i0_reciprocal	62810000.0000
total_estimate	0.8500
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	53.8 Å
skewness	0.195
kurtosis	-0.718
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	7711000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.833

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	SARS-CoV2 KP.3.1.1 spike glycoprotein
formula_weight	144601.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4485

MPMGSLQPLATLYLLGMLVASVLAQCVNLITTTQSYTNFTRGVYYPDKVFRSSVLHLTQDLFLPFFSNVTWFHAISGTNGTKRFDNPVLPFNDGVYFASTEKSNIIRGWIFGTTLDSKTQSLLIVNNATNFVIKVCEFQFCNDPFLDVYHKNNKSWMESESGVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVFKNIDGYFKIYSKHTPIIQRDFPQGFSALEPLVDLPIGINITRFQTLLALNRSYLTPGDSSSGWTAGAADYYVGYLQPRTFLLKYNENGTITDAVDCALDPLSETKCTLKSFTVEKGIYQTSNFRVQPTESIVRFPNVTNLCPFHEVFNATRFASVYAWNRTRISNCVADYSVLYNFASFSTFKCYGVSPTKLNDLCFTNVYADSFVIKGNEVSQIAPGQTGNIADYNYKLPDDFTGCVIAWNSNKLDSKHSGNYDYWYRSLRKSKLKPFERDISTEIYQAGNKPCKGKGPNCYFPLESYGFRPTYGVGHQPYRVVVLSFELLHAPATVCGPKKSTNLVKNKCVNFNFNGLTGTGVLTKSNKKFLPFQQFGRDIVDTTDAVRDPQTLEILDITPCSFGGVSVITPGTNTSNQVAVLYQGVNCTEVSVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEYVNNSYECDIPIGAGVCASYQTQTKSRGSASSVASQSIIAYTMSLGAENSVAYSNNSIAIPTNFTISVTTEILPVSMTKTSVDCTMYICGDSTECSNLLLQYGSFCTQLKRALTGIAVEQDKNTQEVFAQVKQIYKTPPIKYFGGFNFSQILPDPSKPSKRSPIEDLLFNKVTLADAGFIKQYGDCLGDIAARDLICAQKFNGLTVLPPLLTDEMIAQYTSALLAGTITSGWTFGAGPALQIPFPMQMAYRFNGIGVTQNVLYENQKLIANQFNSAIGKIQDSLFSTPSALGKLQDVVNHNAQALNTLVKQLSSKFGAISSVLNDILSRLDPPEAEVQIDRLITGRLQSLQTYVTQQLIRAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFLTQRNFYEPQIITTDNTFVSGNCDVVIGIVNNTVYDPLQLELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQGSGYIPEAPRDGQAYVRKDGEWVFLSTFLSGLEVLFQGPGGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGGSGLNDIFEAQKIEWHEHHHHHHHH

Source

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

Entity 2 non-polymer

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

▶

6. Citations (1)

▶

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	3.37 Å
resolution_method	—
num_particles	36563

fit	/app/data/saxs_computation/ue/9uel/9uel.fit
pddf	/app/data/pr_computation/ue/9uel/9uel.pr.out
profile	/app/data/saxs_computation/ue/9uel/9uel.dat