← Back to search

9r9z

ssRNA-containing helical virus-like particle composed of JGMV coat protein

Method: ELECTRON MICROSCOPY D_max: 207.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r9z
deposition_date	2025-05-20
title	ssRNA-containing helical virus-like particle composed of JGMV coat protein
keywords	Johnsongrass mosaic virus, virus-like particle, potyvirus, coat protein, helical, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	64.05 Å
rg_electron	64.42 Å
i0	15754800000.00
molecular_weight	987020.0 kDa
excluded_volume	1202300 Å³
envelope_volume	1734600 Å³
shell_volume	208090 Å³
envelope_diameter	259.5 Å
shell_rg	75.89 Å
envelope_rg	64.71 Å
shape_rg	64.43 Å
total_rg	64.50 Å
total_atoms	68976
n_residues	8244
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	207.6 Å
rg_real	63.75 Å
rg_real_error	1.06 Å
i0_real	1.5740e+10
i0_real_error	2.8120e+08
rg_reciprocal	64.20 Å
i0_reciprocal	15760000000.0000
total_estimate	0.8417
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	77.8 Å
skewness	0.355
kurtosis	-0.020
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0048
highest_alpha	2026000000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.792; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.609

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Genome polyprotein
formula_weight	33578.3 kDa
src_method	man
entity_count	36

Polymer

type	polypeptide(L)
strand_id	Aa,Ac,Ae,Ag,Ai,Ak,Am,Ao,Aq,As,Au,Aw,Ay,Ba,Bc,Be,Bg,Bi,Bk,Bm,Bo,Bq,Bs,Bu,Bw,By,Ca,Cc,Ce,Cg,Ci,Ck,Cm,Co,Cq,Cs
atom_count	68976

SGNEDAGKQKSATPAANQTASGDGKPVQTTATADNKPSSDNTSNAQGTSQTKGGGESGGTNATATKKDKDVDVGSTGTFVIPKLKKVSPKMRLPMVSNKAILNLDHLIQYKPDQRDISNARATHTQFQFWYNRVKKEYDVDDEQMRILMNGLMVWCIENGTSPDINGYWTMVDGNNQSEFPLKPIVENAKPTLRQCMMHFSDAAEAYIEMRNLDEPYMPRYGLLRNLNDKSLARYAFDFYEINSRTPNRAREAHAQMKAAAIRGSTNHMFGLDGNVGESSENTERHTAADVSRNVHSYRGAKI

Source

organism	Johnsongrass mosaic virus
ncbi_taxonomy_id	31742
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	;RNA (5'-R(PUPUPUPUP*U)-3') ;
formula_weight	1485.9 kDa
src_method	man
entity_count	36

Polymer

type	polyribonucleotide
strand_id	Ab,Ad,Af,Ah,Aj,Al,An,Ap,Ar,At,Av,Ax,Az,Bb,Bd,Bf,Bh,Bj,Bl,Bn,Bp,Br,Bt,Bv,Bx,Bz,Cb,Cd,Cf,Ch,Cj,Cl,Cn,Cp,Cr,Ct

UUUUU

Source

organism	Johnsongrass mosaic virus
ncbi_taxonomy_id	31742
host_organism	Escherichia coli BL21(DE3)

▶

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	3.40 Å
resolution_method	—
num_particles	31352

fit	/app/data/saxs_computation/r9/9r9z/9r9z.fit
pddf	/app/data/pr_computation/r9/9r9z/9r9z.pr.out
profile	/app/data/saxs_computation/r9/9r9z/9r9z.dat

ssRNA-containing helical virus-like particle composed of JGMV coat protein

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

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)