SAXSdb — 9r6s

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1. Structure Basics

entry_id	9r6s
deposition_date	2025-05-13
title	Prefusion stabilized spike glycoprotein of human coronavirus OC43.
keywords	fusion glycoprotein, membrane protein, 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	50.62 Å
rg_electron	50.24 Å
i0	2334780000.00
molecular_weight	404910.0 kDa
excluded_volume	506290 Å³
envelope_volume	701710 Å³
shell_volume	112580 Å³
envelope_diameter	163.6 Å
shell_rg	56.59 Å
envelope_rg	49.73 Å
shape_rg	50.22 Å
total_rg	50.53 Å
total_atoms	28452
n_residues	3519
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	159.7 Å
rg_real	50.48 Å
rg_real_error	1.24 Å
i0_real	2.3350e+09
i0_real_error	4.0580e+07
rg_reciprocal	50.72 Å
i0_reciprocal	2336000000.0000
total_estimate	0.8781
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	61.8 Å
skewness	0.215
kurtosis	-0.516
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	354100000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.660

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	144009.2 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	28452

MFLILLISLPTAFAVIGDLNCTLDPRLKGSFNNRDTGLPSISTDTVDVTNGLGTYYVLDRVYLNTTLFLNGYYPTSGSTYRNMALKGTDLLSTLWFKPPFLSDFINGIFAKVKNTKVFKDGVMYSEFPAITIGSTFVNTSYSVVVQPRTINSTQDGVNKLQGLLEVSVCQYNMCEYPHTICHPNLGNHFKELWHLDTGVVSCLYKRNFTYDVNATYLYFHFYQEGGTFYAYFTDTGFVTKFLFNVHLGMALSHYYVMPLTCIRRPKDGFSLEYWVTPLTPRQYLLAFNQDGIIFNAVDCMSDFMSEIKCKTQSIAPPTGVYELNGYTVQPIADVYRRKPDLPNCNIEAWLNDKSVPSPLNWERKTFSNCNFNMSSLMSFIQADSFTCNNIDAAKIYGMCFSSITIDKFAIPNGRKVDLQLGNRGYLQRSNYRIDTTATSCQLYYNLPAANVSVSRFNPSTWNKRFGFIEDSVFVPQPTGVFTNHSVVYAQHCFKAPKNFCPCSSCPGKNNGIGTCPAGTNSLTCDNLCTLDPITLKAPDTYKCPQSKSLVGIGEHCSGLAVKSDYCGNNSCTCQPQAFLGWSADSCLQGDKCNIFANFILHDVNNGLTCSTDLQKANTEIELGVCVNYDLYGISGQGIFVEVNATYYNSWQNYLYDSNGNLYGFRDYITNRTFMIHSCYSGRVSAAYHANSSEPALLFRNIKCNYVFNNSLTRQLQPINYSFDSYLGCVVNAYNSTAISVQTCDLTVGSGYCVDYSKNSRAGGAITTGYRFVNFEPFTVNSVNDSLEPVGGLYEIQIPSEFTIGNMEEFIQTSSPKVTIDCAAFVCGDYAACKLQLVGYGSFCDNIEAILTEVNELLDTTQLQVANSLMNGVTLSTKLKDGVNFNVDDINFSPVLGCLGSECSKASSRSAIEDLLFDKVKLSDVGFVEAYNNCTGGAEIRDLICIQSYKGIKVLPPLLSENQISGYTLAATSAQLFPPWTANAGVPFYLNVQYRINGLGVTMDVLSQNQKLIANAFNNALHAIQQGFDPTNSALVKIQAVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDPPEAEAQIDKLINGRLTALNAYVSQRLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGLYFIHFNYVPTKYVTAKVSPGLCIAGNRGIAPKSGYFVNVNNTWMYTGSGYYYPEPITENNVVVMSTCAVNYTKAPYVMLNTLIPNLSDFKEELDQWFKNQTSVAPDLSLDYINVTFLDLQVEMNRLQEAIKVLNQSYINLKDKGTYEY

Source

organism	Human coronavirus OC43
common_name	HCoV-OC43
ncbi_taxonomy_id	31631
host_organism	Homo sapiens

Entity 2 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	18

Entity 3 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	33

Entity 4 non-polymer

description	Sapienic acid
formula_weight	254.4 kDa
src_method	syn
entity_count	3

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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	3.10 Å
resolution_method	—
num_particles	92153

fit	/app/data/saxs_computation/r6/9r6s/9r6s.fit
pddf	/app/data/pr_computation/r6/9r6s/9r6s.pr.out
profile	/app/data/saxs_computation/r6/9r6s/9r6s.dat

Prefusion stabilized spike glycoprotein of human coronavirus OC43.

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