SAXSdb — 9qto

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1. Structure Basics

entry_id	9qto
deposition_date	2025-04-09
title	Human alpha7 nicotinic receptor in complex with the E6 nanobody
keywords	Nicotinic receptor, Nanobody, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	37.90 Å
rg_electron	36.96 Å
i0	604638000.00
molecular_weight	199630.0 kDa
excluded_volume	249170 Å³
envelope_volume	334080 Å³
shell_volume	72049 Å³
envelope_diameter	123.4 Å
shell_rg	45.66 Å
envelope_rg	36.29 Å
shape_rg	36.91 Å
total_rg	37.66 Å
total_atoms	14060
n_residues	1660
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	114.6 Å
rg_real	37.57 Å
rg_real_error	0.79 Å
i0_real	6.0460e+08
i0_real_error	1.0710e+07
rg_reciprocal	37.78 Å
i0_reciprocal	604800000.0000
total_estimate	0.8889
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.8 Å
skewness	0.063
kurtosis	-0.424
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	96760000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.919

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Neuronal acetylcholine receptor subunit alpha-7,CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion
formula_weight	42837.7 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	14352

EFQRKLYKELVKNYNPLERPVANDSQPLTVYFSLSLLQIMDVDEKNQVLTTNIWLQMSWTDHYLQWNVSEYPGVKTVRFPDGQIWKPDILLYNSADERFDATFHTNVLVNSSGHCQYLPPGIFKSSCYIDVRWFPFDVQHCKLKFGSWSYGGWSLDLQMQEADISGYIPNGEWDLVGIPGKRSERFYECCKEPYPDVTFTVTMRRRTLYYGLNLLIPCVLISALALLVFLLPADSGEKISLGITVLLSLTVFMLLVAEIMPATSDSVPLIAQYFASTMIIVGLSVVVTVIVLQYHHHDPDGGKMPKWTRVILLNWCAWFLRMKRDGVAVCSEWKFAACVVDRLCLMAFSVFTIICTIGILMSAPNFVEAVSKDFA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Nanobody E6
formula_weight	17089.7 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	F,G,H,I,J

AQLQLVESGGGLVQPGGSLRLSCAASGFTLDYYTIGWFRQAPGKEREGVSCIRGSGGSTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAADFLSTCSLAGYRYEEVWGQGTLVTVSSAHHSEDPSAAAEQKLISEEDLNGAAHHHHHHGS

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Escherichia coli

Entity 3 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	910.8 kDa
src_method	nat
entity_count	5

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	5

Entity 5 branched

description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	732.7 kDa
src_method	man
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	292

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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	2.160 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.16 Å
resolution_method	—
num_particles	445239

fit	/app/data/saxs_computation/qt/9qto/9qto.fit
pddf	/app/data/pr_computation/qt/9qto/9qto.pr.out
profile	/app/data/saxs_computation/qt/9qto/9qto.dat

Human alpha7 nicotinic receptor in complex with the E6 nanobody

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 branched

Entity 4 branched

Entity 5 branched

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)