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9y7x

Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Open State

Method: ELECTRON MICROSCOPY D_max: 128.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y7x
deposition_date	2025-09-11
title	Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Open State
keywords	homopentamer, ion channel, ligand gated ion channel, TRANSPORT PROTEIN; TRANSPORT 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	39.69 Å
rg_electron	39.14 Å
i0	555526000.00
molecular_weight	201610.0 kDa
excluded_volume	255860 Å³
envelope_volume	338500 Å³
shell_volume	70617 Å³
envelope_diameter	132.2 Å
shell_rg	46.17 Å
envelope_rg	38.66 Å
shape_rg	39.17 Å
total_rg	39.46 Å
total_atoms	14199
n_residues	1732
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	128.0 Å
rg_real	39.60 Å
rg_real_error	0.74 Å
i0_real	5.5550e+08
i0_real_error	9.1670e+06
rg_reciprocal	39.66 Å
i0_reciprocal	555600000.0000
total_estimate	0.8108
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.0 Å
skewness	0.337
kurtosis	-0.272
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	78980000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Glycine receptor subunit alpha-2
formula_weight	53782.8 kDa
src_method	man
entity_count	5

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E
atom_count	14199

MNRQLVNILTALFAFFLETNHFRTAFCKDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSVTETTMDYRVNIFLRQQWNDSRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHDVTTDNKLLRISKNGKVLYSIRLTLTLSCPMDLKNFPMDVQTCTMQLESFGYTMNDLIFEWLSDGPVQVAEGLTLPQFILKEEKELGYCTKHYNTGKFTCIEVKFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFAALLEYAAVNFVSRQHKEFLRLRRRQKRQNKEEDVTRESRFNFSGYGMGHCLQVKDGTAVKATPANPLPQPPKDGDAIKKKFVDRAKRIDTISRAAFPLAFLIFNIFYWITYKIIRHEDVHKKLVPRGSHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera aff. frugiperda 1 BOLD-2017

Entity 2 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	10

Entity 3 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	5

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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	3.550 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.55 Å
resolution_method	—
num_particles	16416

fit	/app/data/saxs_computation/y7/9y7x/9y7x.fit
pddf	/app/data/pr_computation/y7/9y7x/9y7x.pr.out
profile	/app/data/saxs_computation/y7/9y7x/9y7x.dat

Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Open State

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