Cryo-EM structure of semi-closed state of Botulinum neurotoxin serotype A at pH 7.4

Method: ELECTRON MICROSCOPY D_max: 112.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vcs
deposition_date	2025-06-06
title	Cryo-EM structure of semi-closed state of Botulinum neurotoxin serotype A at pH 7.4
keywords	Botulinum neurotoxin serotype A, Cryo-EM, TOXIN; TOXIN
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	35.70 Å
rg_electron	34.74 Å
i0	300155000.00
molecular_weight	143790.0 kDa
excluded_volume	181480 Å³
envelope_volume	233310 Å³
shell_volume	54659 Å³
envelope_diameter	114.4 Å
shell_rg	42.36 Å
envelope_rg	34.32 Å
shape_rg	34.72 Å
total_rg	35.36 Å
total_atoms	10158
n_residues	1245
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	112.4 Å
rg_real	35.51 Å
rg_real_error	0.68 Å
i0_real	3.0020e+08
i0_real_error	4.5870e+06
rg_reciprocal	35.63 Å
i0_reciprocal	300200000.0000
total_estimate	0.9001
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.5 Å
skewness	0.119
kurtosis	-0.532
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	67680000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Botulinum neurotoxin type A
formula_weight	151022.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	10158

MPFVNKQFNYKDPVNGVDIAYIKIPNAGQMQPVKAFKIHNKIWVIPERDTFTNPEEGDLNPPPEAKQVPVSYYDSTYLSTDNEKDNYLKGVTKLFERIYSTDLGRMLLTSIVRGIPFWGGSTIDTELKVIDTNCINVIQPDGSYRSEELNLVIIGPSADIIQFECKSFGHEVLNLTRNGYGSTQYIRFSPDFTFGFEESLEVDTNPLLGAGKFATDPAVTLAHELIHAGHRLYGIAINPNRVFKVNTNAYYEMSGLEVSFEELRTFGGHDAKFIDSLQENEFRLYYYNKFKDIASTLNKAKSIVGTTASLQYMKNVFKEKYLLSEDTSGKFSVDKLKFDKLYKMLTEIYTEDNFVKFFKVLNRKTYLNFDKAVFKINIVPKVNYTIYDGFNLRNTNLAANFNGQNTEINNMNFTKLKNFTGLFEFYKLLCVRGIITSKTKSLDKGYNKALNDLCIKVNNWDLFFSPSEDNFTNDLNKGEEITSDTNIEAAEENISLDLIQQYYLTFNFDNEPENISIENLSSDIIGQLELMPNIERFPNGKKYELDKYTMFHYLRAQEFEHGKSRIALTNSVNEALLNPSRVYTFFSSDYVKKVNKATEAAMFLGWVEQLVYDFTDETSEVSTTDKIADITIIIPYIGPALNIGNMLYKDDFVGALIFSGAVILLEFIPEIAIPVLGTFALVSYIANKVLTVQTIDNALSKRNEKWDEVYKYIVTNWLAKVNTQIDLIRKKMKEALENQAEATKAIINYQYNQYTEEEKNNINFNIDDLSSKLNESINKAMININKFLNQCSVSYLMNSMIPYGVKRLEDFDASLKDALLKYIYDNRGTLIGQVDRLKDKVNNTLSTDIPFQLSKYVDNQRLLSTFTEYIKNIINTSILNLRYESNHLIDLSRYASKINIGSKVNFDPIDKNQIQLFNLESSKIEVILKNAIVYNSMYENFSTSFWIRIPKYFNSISLNNEYTIINCMENNSGWKVSLNYGEIIWTLQDTQEIKQRVVFKYSQMINISDYINRWIFVTITNNRLNNSKIYINGRLIDQKPISNLGNIHASNNIMFKLDGCRDTHRYIWIKYFNLFDKELNEKEIKDLYDNQSNSGILKDFWGDYLQYDKPYYMLNLYDPNKYVDVNNVGIRGYMYLKGPRGSVMTTNIYLNSSLYRGTKFIIKKYASGNKDNIVRNNDRVYINVVVKNKEYRLATNASQAGVEKILSALEIPDVGNLSQVVVMKSKNDQGITNKCKMNLQDNNGNDIGFIGFHQFNNIAKLVASNWYNRQIERSSRTLGCSWEFIPVDDGWGERPLLVPRGSHHHHHH

Source

organism	Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)
ncbi_taxonomy_id	441771
host_organism	Escherichia coli BL21(DE3)

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	230734

fit	/app/data/saxs_computation/vc/9vcs/9vcs.fit
pddf	/app/data/pr_computation/vc/9vcs/9vcs.pr.out
profile	/app/data/saxs_computation/vc/9vcs/9vcs.dat

Cryo-EM structure of semi-closed state of Botulinum neurotoxin serotype A at pH 7.4

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)