SAXSdb — 11ov

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1. Structure Basics

entry_id	11ov
deposition_date	2026-03-06
title	Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03
keywords	EV-D68, B3 subclade, 5H03 neutralizing antibody, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	31.48 Å
rg_electron	30.62 Å
i0	156096000.00
molecular_weight	99246.0 kDa
excluded_volume	124080 Å³
envelope_volume	159810 Å³
shell_volume	42598 Å³
envelope_diameter	104.0 Å
shell_rg	38.55 Å
envelope_rg	30.84 Å
shape_rg	30.60 Å
total_rg	31.40 Å
total_atoms	6981
n_residues	897
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	98.7 Å
rg_real	31.32 Å
rg_real_error	0.63 Å
i0_real	1.5610e+08
i0_real_error	2.4540e+06
rg_reciprocal	31.39 Å
i0_reciprocal	156100000.0000
total_estimate	0.9050
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	39.5 Å
skewness	0.158
kurtosis	-0.526
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	27400000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Capsid protein VP1
formula_weight	25735.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6981

VSETLVENFLSRAALVSKRSFEYKDHTSSTAQTDKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSNNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKTGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGKERAPNALNAIIG

Source

organism	Human enterovirus D68
common_name	EV68, EV-68
ncbi_taxonomy_id	42789
host_organism	Homo sapiens

Entity 2 polymer

description	Capsid protein VP0
formula_weight	23797.0 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

ANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEATSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFN

Source

organism	Human enterovirus D68
common_name	EV68, EV-68
ncbi_taxonomy_id	42789
host_organism	Homo sapiens

Entity 3 polymer

description	Capsid protein VP3
formula_weight	27170.9 kDa
ec_number	3.4.22.29,3.6.1.15,3.4.22.28,2.7.7.48
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSITLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQIDHLHGAEAAYQ

Source

organism	Human enterovirus D68
common_name	EV68, EV-68
ncbi_taxonomy_id	42789
host_organism	Homo sapiens

Entity 4 polymer

description	5H03 Fab heavy chain
formula_weight	13768.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	h

EVQLVESGGGLAQPGGSLGLSCAASGFTFSDYAMTWVRQASGKGLEWVGYIRTKYNDHATEYAASVKGRFIISRDDSKNTLFLQMSSLTTEDTAVYYCCREGEFCLGSDCYTSGLDSWGQGVVVTVSS

Source

organism	Macaca mulatta
common_name	Rhesus monkey
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 polymer

description	5H03 Fab light chain
formula_weight	11764.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	l

DIQMTQSPSSLSASVGDTVTITCRASQRFVSSLAWYQQKPGKAPKLLIYSASNLQSGVPSRFSGRKSGTDFILTIRSLQPEDIGNYYCQQFYSYPLTFGGGTKVEIK

Source

organism	Macaca mulatta
common_name	Rhesus monkey
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

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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	2.830 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.83 Å
resolution_method	—
num_particles	48000

fit	/app/data/saxs_computation/1o/11ov/11ov.fit
pddf	/app/data/pr_computation/1o/11ov/11ov.pr.out
profile	/app/data/saxs_computation/1o/11ov/11ov.dat

Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 5H03

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)