SAXSdb — 9r1r

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1. Structure Basics

entry_id	9r1r
deposition_date	2025-04-28
title	Bottlenose dolphin 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	53.38 Å
rg_electron	52.93 Å
i0	2842020000.00
molecular_weight	448170.0 kDa
excluded_volume	560210 Å³
envelope_volume	793280 Å³
shell_volume	120140 Å³
envelope_diameter	174.0 Å
shell_rg	59.01 Å
envelope_rg	52.58 Å
shape_rg	52.94 Å
total_rg	53.07 Å
total_atoms	31461
n_residues	3663
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	172.2 Å
rg_real	53.18 Å
rg_real_error	1.56 Å
i0_real	2.8420e+09
i0_real_error	5.6330e+07
rg_reciprocal	53.53 Å
i0_reciprocal	2843000000.0000
total_estimate	0.8908
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	65.3 Å
skewness	0.147
kurtosis	-0.573
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	402800000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.875

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	150644.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	31461

AEEFLDFDLWPCDTCWNSSLLEENNTYTAAAFHQYGIIPFYYSINWTVVMNYSDGIYDYKWDDVAYNSSNYLAVNVSLVGRNCTANLNETLTEYKGFDFKGFPFSCPDFNVTSIDHGMFGYLLQNVLLGRCTSHLCVVVIPQGRVFFQKDEMWWWSWGDRLGISSHFTRFMVFDRNITVIGIAGNFDLYRLGHDGCKYVTGQSCPGYNWMNVTRIPVVGQVCRWFYADKDNLCNLTRVDNMPKTYYTAELARPATASVIVDGAYKPVYTGKFVDDALGPDYPCPTLSSLQASYVPGDCAIKDWVWIRSFDFKHTYFDAVYVGREEKFSLDAVQIIFRLKPNATYLGLPFCNETHTDKSSSAIIAYLIGGEFYSVDTSTVVVETYNPHIPDPSATPTSASTTQSRTTIYGWQDLRSYNMSCVRFSYELKRVMSVPLSMIRDVIIDVKKRVLSIDGFPVGSLLSDFEFRFSILAMNDTYLAGLKYTTALITFDKGNVRNVIDCNSDSVFDKLRCDLQTDVMSDGFYPVNIKTNEAEENATFIDVEATLANLSLEVFVSSPSHSPACLLKSYKCVDTRYFYLQNYTYSCADNGINDAASSAYCEGRMDTFNKFGVNGLDFRGKCPFSASKVNTGLIFDKICFGVYEQGCQADKVCNFGFYFDDVVFNQYGNKVYYKRQDLGFIDYQFGTLFKNSLVQPNVIQDGCHDYDIYGYKGTGFVKPFFDYSYLNMGGLIMLDSGGFPAVFRHNFALYEVTQCTREVAQLAVASNNALGCYLPKQVNIEGLNDTVDCNITGVFKYCSYGSIQAALSEEVQINVCNPSLMMENSHCINLKGSFMVNEPSVTLNSTTYQPLLGVSGEVVLPRTLMLHTTTEFIQTHSPKIVIDCNKYVCGSSERCRRILIKYGGFCESIIRLLNGVNMADDVSVTDFLDNLNSFDNISISLQSLNDSFGSFDGYGFQKFLPKSFDFGSGDPRQSRSTIEDLLFDKVTTVGLGTVDADYDKCTKGLSVADLVCAQYYNGIMVLPGVADAEKMAMYTGALVGGMALGGITAAASIPFATQIQARVNYLALTQNAIQENQKIIVQQFNKAIDSMTSAFESVNAGFSAVSSAITEIQNTVNAQSQALTKLLGQLNYNFGATTSSIKELYERLAPPEADIQVDRLINGRLTALSAFVAARQVEASRVASQRVLAAEKINECVKSTSNRYGFCGNGTHIISFPQNAPNGMLFVHFSLVPNETITVYGIIGLCLNNSIGIVPAKDRGIFIKCSNGSYCPEFENSFNMTKDGNVTFPFAITSREQYNPRQITTGDIQMLTSCNSSYTHIEWSQLPLVAPPYKDFDQEFEELYEKWNY

Source

organism	Bottlenose dolphin coronavirus HKU22
ncbi_taxonomy_id	1433215
host_organism	Homo sapiens

Entity 2 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	18

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	27

Entity 4 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 5 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 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1057.0 kDa
src_method	man
entity_count	3

Entity 7 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	36

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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	2.650 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.65 Å
resolution_method	—
num_particles	321116

fit	/app/data/saxs_computation/r1/9r1r/9r1r.fit
pddf	/app/data/pr_computation/r1/9r1r/9r1r.pr.out
profile	/app/data/saxs_computation/r1/9r1r/9r1r.dat

Bottlenose dolphin coronavirus spike glycoprotein

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