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9r1q

Beluga whale coronavirus spike glycoprotein

Method: ELECTRON MICROSCOPY D_max: 186.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r1q
deposition_date	2025-04-28
title	Beluga whale coronavirus spike glycoprotein
keywords	spike, glycoprotein, coronavirus, 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	54.53 Å
rg_electron	54.27 Å
i0	2995650000.00
molecular_weight	459750.0 kDa
excluded_volume	574690 Å³
envelope_volume	837580 Å³
shell_volume	123820 Å³
envelope_diameter	197.9 Å
shell_rg	59.86 Å
envelope_rg	54.42 Å
shape_rg	54.27 Å
total_rg	54.45 Å
total_atoms	38610
n_residues	3777
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	186.9 Å
rg_real	54.44 Å
rg_real_error	1.63 Å
i0_real	2.9960e+09
i0_real_error	5.7870e+07
rg_reciprocal	54.60 Å
i0_reciprocal	2996000000.0000
total_estimate	0.8699
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.5 Å
skewness	0.313
kurtosis	-0.254
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	483900000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.897

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4. Crystallography & Experiment

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5. Entities & Polymer Info (12)

Entity 1 polymer

description	Spike protein
formula_weight	153930.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	38610

IDEGLWPAGMWYSHLLQENNTYTVAAFQEHAILPSYVNNNWTVITNFTAENATQLEWDDPYYNSTLFSYVNITMVGDNCIGNFTNRTLGELGDIDYFPFNCTNVTNEFRTNYGYFIQNVMVARCLSSLCAVIIPKGRVFFEKNEMWWWSWQDRYQPGNYTFRHERFMSLSQNITVIGLAGNFSLFGLGQTININSASYDWGTVIRGRLDDRICELQMTGADLCNLTRVDTSSDAFYTAGLVRPASAALIADGAYKPIFTGVFHDNETHQVLYENATIKPSVRSFQVKNNDFDALYVGRKEKFSIDAVTIIFRLKETSTYLDLPFCNETRVDKSDKAIIGYLIGGDFYSVDVSSIVIERYNPPQPNATSIPTTISTVSTTTSGWEDLRSLNMSCVRFDYKLKKVMSVPLPMVKAFIIDFKQRQLAIDGFPVGALIADFEFRFSIVAMPQTFISTLNYTTALVTFDKGNVRSVIDCNSEKPFDRLRCDLQTDVVSDGFYPVNIKTNEAKENTTFIDVPATLANLTLEVFVSSPEQSPACVIKSYKCVDTRYFYISDYSYSCAENGIPNDAAGAAYCRGVLDQINNYGVRGMDFKGKCPFAGSKVNSGLTFDKICFGVYEQGCQSDKACRFGFYFDNVQFSQYGNKLYYKPQDLGFIDYQFGTLFKNSLVQSNIIQEGCHDYDIYGYKGTGVVKPFSDYSYLQTGGLIMLDSGGFPSLFRYNFALYEVTQCTREVAQLAVASNNAIGYYLPKQVTIDGVNASTSCNTTGAFKYCYYDDVIHVGRDVSNVTINVCNPSLMMENSHCINIQGNFMVNEPAITFNSTQYQPLLGVSGDVQLPRTLMLHTTTEFIQTHSPKIVIDCTKYVCGSSERCRRILVKYGGFCESIMRLLNGVNMADDVSVTDFLDNFNSFDNISVSLQNLNASFGQFEGYGFQKFLPKSFDFDGSDPRDARSTIEDILFDKVTTVGLGTVDADYDKCTKGLSVADLVCAQYYNGIMVLPGVADAEKMAMYTGALVGGMVLGGITSAAAIPFATQIQARVNYLALTQNAIQENQKIIVQQFNKAIDSMTSAFQSVNEGFSAVSSAITEVQNAVNAQSQALTKLLGQLNYNFGATTSSIKELYERLAPPEADVQVDRLINGRLTALSAFVAARQVEAAKVASQRVLAAEKINECVKSTSNRYGFCGNGAHIISFPQNAPNGMLFVHFSLVPNETITVKGIIGLCLNNSIGIVPAKDRGMFIQCSNGTYCPEFENSFNESKNGNVTFPFAITSREQYNPRQITTGDIQMLTSCNSGYTHIEWSQLPLVAPPYDDFDKEFDKLYEKWNYTLEELEKLNVTFPYLNVSEQIDIINSAMENIKSQIQNLNSSYIDLEWLNKYER

Source

organism	Beluga whale coronavirus SW1
ncbi_taxonomy_id	694015
host_organism	Homo sapiens

Entity 2 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	3

Entity 3 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	9

Entity 4 branched

description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	894.8 kDa
src_method	man
entity_count	3

Entity 5 branched

description	;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	748.7 kDa
src_method	man
entity_count	6

Entity 6 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	man
entity_count	3

Entity 7 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1057.0 kDa
src_method	man
entity_count	9

Entity 8 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	6

Entity 9 branched

description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	732.7 kDa
src_method	man
entity_count	3

Entity 10 branched

description	alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	367.3 kDa
src_method	man
entity_count	3

Entity 11 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	3

Entity 12 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	30

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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	2.240 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.24 Å
resolution_method	—
num_particles	687529

fit	/app/data/saxs_computation/r1/9r1q/9r1q.fit
pddf	/app/data/pr_computation/r1/9r1q/9r1q.pr.out
profile	/app/data/saxs_computation/r1/9r1q/9r1q.dat