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9y8z

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

Method: ELECTRON MICROSCOPY D_max: 132.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9y8z
deposition_date	2025-09-11
title	Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine 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	39.91 Å
rg_electron	39.49 Å
i0	550719000.00
molecular_weight	210890.0 kDa
excluded_volume	271570 Å³
envelope_volume	346410 Å³
shell_volume	71207 Å³
envelope_diameter	131.2 Å
shell_rg	46.56 Å
envelope_rg	39.32 Å
shape_rg	39.52 Å
total_rg	39.78 Å
total_atoms	14860
n_residues	1745
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	132.6 Å
rg_real	39.88 Å
rg_real_error	1.23 Å
i0_real	5.5070e+08
i0_real_error	9.7890e+06
rg_reciprocal	39.90 Å
i0_reciprocal	550700000.0000
total_estimate	0.8723
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.4 Å
skewness	0.376
kurtosis	-0.276
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	92210000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.908

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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	14860

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	30

Entity 4 non-polymer

description	CHOLESTEROL
formula_weight	386.7 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	2.500 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.50 Å
resolution_method	—
num_particles	121954

fit	/app/data/saxs_computation/y8/9y8z/9y8z.fit
pddf	/app/data/pr_computation/y8/9y8z/9y8z.pr.out
profile	/app/data/saxs_computation/y8/9y8z/9y8z.dat

Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine 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