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9y95

Homomeric Glycine Receptor alpha2 with PTX in an Apo State

Method: ELECTRON MICROSCOPY D_max: 126.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y95
deposition_date	2025-09-13
title	Homomeric Glycine Receptor alpha2 with PTX in an Apo 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	39.49 Å
rg_electron	38.99 Å
i0	540358000.00
molecular_weight	204030.0 kDa
excluded_volume	260910 Å³
envelope_volume	338130 Å³
shell_volume	70236 Å³
envelope_diameter	127.1 Å
shell_rg	46.47 Å
envelope_rg	38.74 Å
shape_rg	39.01 Å
total_rg	39.35 Å
total_atoms	14367
n_residues	1718
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	126.2 Å
rg_real	39.42 Å
rg_real_error	0.80 Å
i0_real	5.4040e+08
i0_real_error	8.6380e+06
rg_reciprocal	39.46 Å
i0_reciprocal	540400000.0000
total_estimate	0.8680
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.3 Å
skewness	0.346
kurtosis	-0.297
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	94830000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.665

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	14367

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	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	678.9 kDa
src_method	syn
entity_count	20

Entity 4 non-polymer

description	;(1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione ;
formula_weight	292.3 kDa
src_method	man
entity_count	1

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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	3.450 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.45 Å
resolution_method	—
num_particles	102851

fit	/app/data/saxs_computation/y9/9y95/9y95.fit
pddf	/app/data/pr_computation/y9/9y95/9y95.pr.out
profile	/app/data/saxs_computation/y9/9y95/9y95.dat

Homomeric Glycine Receptor alpha2 with PTX in an Apo 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