SAXSdb — 11lt

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1. Structure Basics

entry_id	11lt
deposition_date	2026-03-03
title	Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 1E11
keywords	EV-D68, B3 subclade, Virus-like particle vaccine, 1E11 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	31.73 Å
rg_electron	30.91 Å
i0	155930000.00
molecular_weight	99402.0 kDa
excluded_volume	124270 Å³
envelope_volume	157120 Å³
shell_volume	41506 Å³
envelope_diameter	101.0 Å
shell_rg	38.58 Å
envelope_rg	31.24 Å
shape_rg	30.88 Å
total_rg	31.69 Å
total_atoms	7004
n_residues	895
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	99.9 Å
rg_real	31.60 Å
rg_real_error	0.85 Å
i0_real	1.5590e+08
i0_real_error	2.2500e+06
rg_reciprocal	31.66 Å
i0_reciprocal	155900000.0000
total_estimate	0.9067
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	40.0 Å
skewness	0.182
kurtosis	-0.559
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	33840000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.947

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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	7004

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	1E11 Fab heavy chain
formula_weight	13879.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVKLQQWGEGLVKPSETLSLTCAVYGGSIHGYYYWSWIRQPPGKGLEWIGYIYGDNFSTNYNPSLKNRVTISKDTPRNQFSLRLTSVTAADTALYFCAREAGSRNAYNWFDVWGPGVRVAVTS

Source

organism	Macaca mulatta
common_name	Rhesus monkey
ncbi_taxonomy_id	9544
host_organism	Homo sapiens

Entity 5 polymer

description	1E11 Fab light chain
formula_weight	11805.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QSALTQPPSVSRSLGQSVTISCTATSSDITFYYGVSWYQHHSGTAPRLLIYEVNERPSGVSNRFSGSKSGNTASLTISGVQADDEADYYCGTYRTGNTWVFGGGTRLTVL

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	2.630 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.63 Å
resolution_method	—
num_particles	724000

fit	/app/data/saxs_computation/1l/11lt/11lt.fit
pddf	/app/data/pr_computation/1l/11lt/11lt.pr.out
profile	/app/data/saxs_computation/1l/11lt/11lt.dat

Cryo-EM structure of EV-D68 B3 VLP bound by neutralizing antibody 1E11

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)