Cryo-EM structure of modified JEV virus E protein dimer

Method: ELECTRON MICROSCOPY D_max: 151.5 Å Quality: SUSPICIOUS

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9pl9
deposition_date	2025-07-15
title	Cryo-EM structure of modified JEV virus E protein dimer
keywords	VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	44.65 Å
rg_electron	45.67 Å
i0	124652000.00
molecular_weight	87946.0 kDa
excluded_volume	109000 Å³
envelope_volume	166480 Å³
shell_volume	35053 Å³
envelope_diameter	159.0 Å
shell_rg	41.76 Å
envelope_rg	44.93 Å
shape_rg	45.63 Å
total_rg	45.55 Å
total_atoms	6160
n_residues	802
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

▼

3. P(r) Analysis (GNOM)

dmax	151.5 Å
rg_real	45.44 Å
rg_real_error	2.18 Å
i0_real	1.2470e+08
i0_real_error	2.6440e+06
rg_reciprocal	44.66 Å
i0_reciprocal	124500000.0000
total_estimate	0.4926
solution_quality	SUSPICIOUS a SUSPICIOUS solution
n_peaks	2
r_peak_primary	34.6 Å
skewness	0.594
kurtosis	-0.469
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	7359000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 1.000; Sysdev: 0.010; Positv: 1.000; Valcen: 0.339; Smooth: 0.147

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

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	4.180 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.18 Å
resolution_method	—
num_particles	172829

description	Genome polyprotein
formula_weight	46053.7 kDa
src_method	man
entity_count	2

Cryo-EM structure of modified JEV virus E protein dimer

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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 branched

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Japanese encephalitis virus
ncbi_taxonomy_id	11072
host_organism	Drosophila

description	;alpha-D-mannopyranose-(1-3)-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	2

fit	/app/data/saxs_computation/pl/9pl9/9pl9.fit
pddf	/app/data/pr_computation/pl/9pl9/9pl9.pr.out
profile	/app/data/saxs_computation/pl/9pl9/9pl9.dat

type	polypeptide(L)
strand_id	A,B
atom_count	6160