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9r6q

;Local refinement of the N-terminal domain (NTD) and receptor binding domain (RBD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the closed conformation bound to 9-O-Ac-Sia ;

Method: ELECTRON MICROSCOPY D_max: 87.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6q
deposition_date	2025-05-13
title	;Local refinement of the N-terminal domain (NTD) and receptor binding domain (RBD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the closed conformation bound to 9-O-Ac-Sia ;
keywords	Coronavirus, Spike, 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	27.51 Å
rg_electron	26.40 Å
i0	62178900.00
molecular_weight	60920.0 kDa
excluded_volume	75922 Å³
envelope_volume	97168 Å³
shell_volume	30913 Å³
envelope_diameter	93.6 Å
shell_rg	33.45 Å
envelope_rg	26.29 Å
shape_rg	26.35 Å
total_rg	27.33 Å
total_atoms	4280
n_residues	535
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	87.9 Å
rg_real	27.40 Å
rg_real_error	0.54 Å
i0_real	6.2180e+07
i0_real_error	8.6820e+05
rg_reciprocal	27.44 Å
i0_reciprocal	62180000.0000
total_estimate	0.9069
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.167
kurtosis	-0.575
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	9793000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.989

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4280

VLGDLKCNTSSINDVDTGVPSISSEVVDVTNGLGTFYVLDRVYLNTTLLLNGYYPISGATFRNMALKGTRLLSTLWFKPPFLSPFNDGIFAKVKNSRFFKDGVIYSEFPAITIGSTFVNTSYSIVVEPHTLLINGNLQGLLQISVCQYTMCEYPHTICHPNLGNQRIELWHYDTDVVSCLYRRNFTYDVNADYLYFHFYQEGGTFYAYFTDTGFVTKFLFKLYLGTVLSHYYVMPLTCDSALSLEYWVTPLTTRQFLLAFDQDGVLYHAVDCASDFMSEIMCKTSSITPPTGVYELNGYTVQPVATVYRRIPDLPNCDIEAWLNSKTVSSPLNWERKIFSNCNFNMGRLMSFIQADSFGCNNIDASRLYGMCFGSITIDKFAIPNSRKVDLQVGKSGYLQSFNYKIDTAVSSCQLYYSLPAANVSVTHYNPSSWNRRYGFNNQSFGSRGLHDAVYSQQCFNTPNTYCPCRTSQCIGGAGTGTCPVGTTVRKCFAAVTNATKCTCWCQPDPSTYKGVNAWTCPQSKVSIQPGQHCPGLGLVEDDCSGNPCTCKPQAFIGWSSETCLQNGRCNIFANFILNDVNSGTTCSTDLQQGNTNITTDVCVNYDLYGITGQGILIEVNATYYNSWQNLLYDSSGNLYGFRDYLSNRTFLIRSCYSGRVSAVFHANSSEPALMFRNLKCSHVFNNTILRQIQLVNYFDSYLGCVVNAYNNTASAVSTCDLTVGSGYCVDYVTALRSRRSFTTGYRFTNFEPFAVNLVNDSIEPVGGLYEIQIPSEFTIGNLEEFIQTSSPKVTIDCATFVCGDYAACRQQLAEYGSFCENINAILIEVNELLDTTQLQVANSLMNGVTLSTKIKDGINFNVDDINFSPVLGCLGSECNRASTRSAIEDLLFDKVKLSDVGFVQAYNNCTGGAEIRDLICVQSYNGIKVLPPLLSENQISGYTLAATAASLFPPWTAAAGVPFYLNVQYRINGLGVTMDVLSQNQKLIASAFNNALDAIQEGFDATNSALVKIQSVVNANAEALNNLLQQLSNRFGAISASLQEILSRLDALEAKAQIDRLINGRLTALNAYVSQQLSDSTLVKFSAAQAMEKVNECVKSQSSRINFCGNGNHIISLVQNAPYGLYFIHFSYVPTKYVTAKVSPGLCIAGDIGISPKSGYFINVNNSWMFTGSGYYYPEPITQNNVVMMSTCAVNYTKAPDLMLNTSTPNLPDFKEELYQWFKNQSSVAPDLSLDYINVTFLDLQDEMNRLQEAIKVLNGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGSLVPRGSHHHHHHHHSAWSHPQFEKGTGGLNDIFEAQKIEWHE

Source

organism	Porcine hemagglutinating encephalomyelitis virus
ncbi_taxonomy_id	42005
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	1

Entity 3 non-polymer

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

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	1

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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	3.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.50 Å
resolution_method	—
num_particles	203953

fit	/app/data/saxs_computation/r6/9r6q/9r6q.fit
pddf	/app/data/pr_computation/r6/9r6q/9r6q.pr.out
profile	/app/data/saxs_computation/r6/9r6q/9r6q.dat

;Local refinement of the N-terminal domain (NTD) and receptor binding domain (RBD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike 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