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9y7w

Homomeric Glycine Receptor alpha2 with 1 mM Glycine in an Open State

Method: ELECTRON MICROSCOPY D_max: 130.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y7w
deposition_date	2025-09-11
title	Homomeric Glycine Receptor alpha2 with 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	39.53 Å
rg_electron	38.99 Å
i0	554215000.00
molecular_weight	201480.0 kDa
excluded_volume	255720 Å³
envelope_volume	333420 Å³
shell_volume	69886 Å³
envelope_diameter	131.1 Å
shell_rg	46.00 Å
envelope_rg	38.53 Å
shape_rg	39.01 Å
total_rg	39.31 Å
total_atoms	14190
n_residues	1731
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	130.6 Å
rg_real	39.44 Å
rg_real_error	1.43 Å
i0_real	5.5420e+08
i0_real_error	1.0220e+07
rg_reciprocal	39.50 Å
i0_reciprocal	554200000.0000
total_estimate	0.8725
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	49.0 Å
skewness	0.341
kurtosis	-0.268
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	73970000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.919

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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	14190

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	3.190 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.19 Å
resolution_method	—
num_particles	53568

fit	/app/data/saxs_computation/y7/9y7w/9y7w.fit
pddf	/app/data/pr_computation/y7/9y7w/9y7w.pr.out
profile	/app/data/saxs_computation/y7/9y7w/9y7w.dat

Homomeric Glycine Receptor alpha2 with 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