SAXSdb — 9z6v

▼

1. Structure Basics

entry_id	9z6v
deposition_date	2025-11-14
title	The structure of TMD with 3 TARPs and 1 CNIH from all native AMPA receptor subtypes
keywords	Ionotropic glutamate receptor AMPA receptor, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	34.67 Å
rg_electron	33.36 Å
i0	184357000.00
molecular_weight	124230.0 kDa
excluded_volume	161590 Å³
envelope_volume	204060 Å³
shell_volume	50011 Å³
envelope_diameter	114.0 Å
shell_rg	40.77 Å
envelope_rg	33.66 Å
shape_rg	33.35 Å
total_rg	34.00 Å
total_atoms	8797
n_residues	1138
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

▼

3. P(r) Analysis (GNOM)

dmax	107.5 Å
rg_real	34.53 Å
rg_real_error	0.65 Å
i0_real	1.8440e+08
i0_real_error	2.6280e+06
rg_reciprocal	34.62 Å
i0_reciprocal	184400000.0000
total_estimate	0.8936
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.4 Å
skewness	0.169
kurtosis	-0.379
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	16340000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.873

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 polymer

description	Mix of AMPAR subunit (GluA1, GluA2, GluA3 and GluA4)
formula_weight	29723.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	8797

KPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSXXXXXXXXXXXXXXXXXXXXXNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSALSLSNVAGVFYILAGGLGLAMAVALIEFCYKSRA

Entity 2 polymer

description	Glutamate receptor 2
formula_weight	29838.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

KPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSXXXXXXXXXXXXXXXXXXXXXNEFGIFNSLWFSLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRA

Entity 3 polymer

description	Mix of protein cornichon homolog 2 and 3
formula_weight	17901.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

AFTFAAFCYMLALVLCAALIFFAIWHIIAFDELRTDFKAPIDQANPAAARERLANIERICALLRKLVAPEYSIHALFCAMFLCAAEWATLGLNAPLLFYHAWRYFHAPADASEAAYDAAAAMNADALAYCQKEAWCKLAFYLLSFFYYLYAMAYTLVSA

Entity 4 polymer

description	Mix of voltage-dependent calcium channel gamma subunits
formula_weight	21045.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

VQALLTTAGAFAAFALMTIAAATDYWLYARAAACATAAAAXXXXXXXXXXXAAAAKKAAAAATHSGLWRACCLEGAAAGACAAIAHFPEDADYAADAAEYALRAVRASSIFPILSAILLAAGGACAAASAAYKAAANIILAAGIAFVAAGLSNIIGAIVYISANAGAPAAAAAAAKKNAYSYGWSFYFGALSFIAAEAAGVLAVAAAIARAAAAAAAARAA

Entity 5 polymer

description	Voltage-dependent calcium channel gamma-8 subunit
formula_weight	43371.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

ESLKRWNEERGLWCEKGVQVLLTTIGAFSAFGLMTIAISTDYWLYTRALICNTTNLTAGDDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSDLLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFASTDISMYTLSRDPSKGSVAAGLASAGGGGSGAGVGAYGGAAGAAGGGGAGSERDRGSSAGFLTLHNAFPKEAASGVTVTVTGPPAAPAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKTTPV

Entity 6 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	23

Entity 7 non-polymer

description	TETRADECANE
formula_weight	198.4 kDa
src_method	syn
entity_count	3

Entity 8 non-polymer

description	6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol
formula_weight	328.7 kDa
src_method	syn
entity_count	2

▶

6. Citations (1)

▶

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	triclinic

resolution	3.00 Å
resolution_method	—
num_particles	82389

fit	/app/data/saxs_computation/z6/9z6v/9z6v.fit
pddf	/app/data/pr_computation/z6/9z6v/9z6v.pr.out
profile	/app/data/saxs_computation/z6/9z6v/9z6v.dat

The structure of TMD with 3 TARPs and 1 CNIH from all native AMPA receptor subtypes

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)