← Back to search

9tkm

CryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion

Method: ELECTRON MICROSCOPY D_max: 101.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9tkm
deposition_date	2025-12-10
title	CryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion
keywords	CVB1, VLP, vaccine candidate, enterovirus, 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	29.26 Å
rg_electron	28.44 Å
i0	90292900.00
molecular_weight	74928.0 kDa
excluded_volume	93660 Å³
envelope_volume	115240 Å³
shell_volume	34338 Å³
envelope_diameter	107.1 Å
shell_rg	35.05 Å
envelope_rg	29.26 Å
shape_rg	28.43 Å
total_rg	29.10 Å
total_atoms	10401
n_residues	675
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	101.7 Å
rg_real	29.34 Å
rg_real_error	0.91 Å
i0_real	9.0290e+07
i0_real_error	1.5490e+06
rg_reciprocal	29.30 Å
i0_reciprocal	90290000.0000
total_estimate	0.8620
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.9 Å
skewness	0.479
kurtosis	-0.120
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	18940000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.763; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.945

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Capsid protein VP1
formula_weight	31197.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	10401

GPVEESVERAMVRVADTVSSRPTNSESIPALTAAETGHTSQVVPSDTMQTRHVKNYHSRSESSIENFLCRAACVYYATYTNNSEKGYAEWVINTRQVAQLRRKLELFTYLRFDLELTFVITSAQQPSTATSVDAPVQTHQIMYVPPGGPVPTKVTDYAWQTSTNPSVFWTEGNAPPRMSIPFISIGNAYSCFYDGWTQFSRNGVYGINTLNNMGTLYMRHVNEAGQGPIKSTVRIYFKPKHVKAWVPRPPRLCQYEKQKNVNFTPTGVTTTRVGITTT

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 2 polymer

description	Capsid protein VP2
formula_weight	29137.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	2

SPSAEECGFSDRVRSITLGNSTITTQECANVVVGYGVWPEYLKDNEATAEDQPTQPDVATCRFYTLESVQWMKNSAGWWWKLPDALSQMGLFGQNMQYHYLGRTGYTIHVQCNASKFHQGCLLVVCVPEAEMGCSNLNNTPEFAELSGGDTARMFTDTQIGETNSKKVQTAVWNAGMGVGVGNLTIYPHQWINLRTNNSATIVMPYINSVPMDNMFRHNNLTLMIIPFVPLNYSEGSSPYVPITVTIAPMCAEYNGLRLASSQ

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

Entity 3 polymer

description	Capsid protein VP3
formula_weight	26268.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	3

GLPVMTTPGSTQFLTSDDFQSPSAMPQFDVTPEMQIPGRVNNLMEIAEVDSVVPVNNTEANVNSLKAYQIPVQSNSDNGKQVFGFPLQPGANGVLNRTLLGEILNYYTHWSGSIKLTFMFCGSAMATGKFLLAYSPPGAGVPKNRKDAMLGTHVIWDVGLQSSCVLCVPWISQTHYRYVVEDEYTAAGYITCWYQTNIVVPADVQSSCDILCFVSACNDFSVRMLKDTPFIRQDTFYQ

Source

organism	Coxsackievirus B1
ncbi_taxonomy_id	12071
host_organism	Trichoplusia ni

▶

6. Citations (1)

▶

resolution	2.70 Å
resolution_method	—
num_particles	53853

fit	/app/data/saxs_computation/tk/9tkm/9tkm.fit
pddf	/app/data/pr_computation/tk/9tkm/9tkm.pr.out
profile	/app/data/saxs_computation/tk/9tkm/9tkm.dat

CryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)