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9r6p

Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the closed conformation bound to 9-O-Ac-Sia.

Method: ELECTRON MICROSCOPY D_max: 168.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6p
deposition_date	2025-05-13
title	Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the closed conformation bound to 9-O-Ac-Sia.
keywords	coronavirus, glycoprotein, entry, 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	51.48 Å
rg_electron	51.09 Å
i0	2191290000.00
molecular_weight	390490.0 kDa
excluded_volume	487540 Å³
envelope_volume	710230 Å³
shell_volume	113040 Å³
envelope_diameter	171.7 Å
shell_rg	57.01 Å
envelope_rg	50.15 Å
shape_rg	51.07 Å
total_rg	51.37 Å
total_atoms	27448
n_residues	3462
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	168.5 Å
rg_real	51.36 Å
rg_real_error	1.07 Å
i0_real	2.1910e+09
i0_real_error	3.7330e+07
rg_reciprocal	51.57 Å
i0_reciprocal	2192000000.0000
total_estimate	0.8158
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	59.8 Å
skewness	0.261
kurtosis	-0.427
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	311000000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Spike glycoprotein
formula_weight	147884.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,H
atom_count	27448

VLGDLKCNTSSINDVDTGVPSISSEVVDVTNGLGTFYVLDRVYLNTTLLLNGYYPISGATFRNMALKGTRLLSTLWFKPPFLSPFNDGIFAKVKNSRFFKDGVIYSEFPAITIGSTFVNTSYSIVVEPHTLLINGNLQGLLQISVCQYTMCEYPHTICHPNLGNQRIELWHYDTDVVSCLYRRNFTYDVNADYLYFHFYQEGGTFYAYFTDTGFVTKFLFKLYLGTVLSHYYVMPLTCDSALSLEYWVTPLTTRQFLLAFDQDGVLYHAVDCASDFMSEIMCKTSSITPPTGVYELNGYTVQPVATVYRRIPDLPNCDIEAWLNSKTVSSPLNWERKIFSNCNFNMGRLMSFIQADSFGCNNIDASRLYGMCFGSITIDKFAIPNSRKVDLQVGKSGYLQSFNYKIDTAVSSCQLYYSLPAANVSVTHYNPSSWNRRYGFNNQSFGSRGLHDAVYSQQCFNTPNTYCPCRTSQCIGGAGTGTCPVGTTVRKCFAAVTNATKCTCWCQPDPSTYKGVNAWTCPQSKVSIQPGQHCPGLGLVEDDCSGNPCTCKPQAFIGWSSETCLQNGRCNIFANFILNDVNSGTTCSTDLQQGNTNITTDVCVNYDLYGITGQGILIEVNATYYNSWQNLLYDSSGNLYGFRDYLSNRTFLIRSCYSGRVSAVFHANSSEPALMFRNLKCSHVFNNTILRQIQLVNYFDSYLGCVVNAYNNTASAVSTCDLTVGSGYCVDYVTALRSRRSFTTGYRFTNFEPFAVNLVNDSIEPVGGLYEIQIPSEFTIGNLEEFIQTSSPKVTIDCATFVCGDYAACRQQLAEYGSFCENINAILIEVNELLDTTQLQVANSLMNGVTLSTKIKDGINFNVDDINFSPVLGCLGSECNRASTRSAIEDLLFDKVKLSDVGFVQAYNNCTGGAEIRDLICVQSYNGIKVLPPLLSENQISGYTLAATAASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIASAFNNALDAIQEGFDATNSALVKIQSVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAKAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTAKVSPGLCIAGDIGISPKSGYFINVNNSWMFTGSGYYYPEPITQNNVVMMSTCAVNYTKAPDLMLNTSTPNLPDFKEELYQWFKNQSSVAPDLSLDYINVTFLDLQDEMNRLQEAIKVLNGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGSLVPRGSHHHHHHHHSAWSHPQFEKGTGGLNDIFEAQKIEWHE

Source

organism	Porcine hemagglutinating encephalomyelitis virus
ncbi_taxonomy_id	42005
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	3

Entity 3 non-polymer

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

Entity 4 non-polymer

description	9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
formula_weight	351.3 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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	67985

fit	/app/data/saxs_computation/r6/9r6p/9r6p.fit
pddf	/app/data/pr_computation/r6/9r6p/9r6p.pr.out
profile	/app/data/saxs_computation/r6/9r6p/9r6p.dat

Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the closed conformation bound to 9-O-Ac-Sia.

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