SAXSdb — 9zkm

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1. Structure Basics

entry_id	9zkm
deposition_date	2025-12-07
title	The LBD-TMD structure of native mouse AMPAR with 4 TARPs
keywords	iGluR, AMPA receptors, SIGNALING PROTEIN; SIGNALING 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	44.01 Å
rg_electron	43.21 Å
i0	784190000.00
molecular_weight	252830.0 kDa
excluded_volume	325250 Å³
envelope_volume	446640 Å³
shell_volume	83323 Å³
envelope_diameter	144.7 Å
shell_rg	50.34 Å
envelope_rg	42.42 Å
shape_rg	43.21 Å
total_rg	43.54 Å
total_atoms	17822
n_residues	2316
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	138.6 Å
rg_real	43.80 Å
rg_real_error	0.72 Å
i0_real	7.8420e+08
i0_real_error	1.1340e+07
rg_reciprocal	44.01 Å
i0_reciprocal	784400000.0000
total_estimate	0.8883
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.9 Å
skewness	0.158
kurtosis	-0.471
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0001
highest_alpha	90400000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.807

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Glutamate receptor 1
formula_weight	55260.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	17822

TYIVTTILEDPYVMLKKNANQFEGNDRYEGYCVELAAEIAKHVGYSYRLEIVSDGKYGARDPDTKAWNGMVGELVYGRADVAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHSEEFEEGRDQTTSDQSNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLEAGSTKEFFRRSKIAVFEKMWTYMKSAEPSVFVRTTEEGMIRVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSALRGPVNLAVLKLSEQGVLDKLKSKWWYDKGECGSKDSGSKDKTSALSLSNVAGVFYILIGGLGLAMLVALIEFCYKSRSESKRMKGFCLIPQQSINEAIRTSTLPRNSGAGASGGSGSGENGRVVSQDFPKSMQSIPCMSHSSGMPLGATGL

Entity 2 polymer

description	Glutamate receptor 2
formula_weight	52118.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

VVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMRQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLRNAVNLAVLKLNEQGLLDKLKNKWWYDKGECGSGGGDSKEKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKVAKNAQNINPSSSQNSQNFATYKEGYNVYGIESVKI

Entity 3 polymer

description	Voltage-dependent calcium channel gamma-2 subunit
formula_weight	35938.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

MGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSSSRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVHNCIQKDSKDSLHANTANRRTTPV

Entity 4 polymer

description	Voltage-dependent calcium channel gamma-8 subunit
formula_weight	43502.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,H

MESLKRWNEERGLWCEKGVQVLLTTIGAFSAFGLMTIAISTDYWLYTRALICNTTNLTAGDDGPPHRGGSGSSEKKDPGGLTHSGLWRICCLEGLKRGVCVKINHFPEDTDYDHDSAEYLLRVVRASSIFPILSAILLLLGGVCVAASRVYKSKRNIILGAGILFVAAGLSNIIGVIVYISANAGEPGPKRDEEKKNHYSYGWSFYFGGLSFILAEVIGVLAVNIYIERSREAHCQSRSDLLKAGGGAGGSGGSGPSAILRLPSYRFRYRRRSRSSSRGSSEASPSRDASPGGPGGPGFASTDISMYTLSRDPSKGSVAAGLASAGGGGSGAGVGAYGGAAGAAGGGGAGSERDRGSSAGFLTLHNAFPKEAASGVTVTVTGPPAAPAPAPAPPAPAAPAPGTLSKEAAASNTNTLNRKTTPV

Entity 5 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	12

Entity 6 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	8

Entity 7 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	8

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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	3.130 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.13 Å
resolution_method	—
num_particles	112093

fit	/app/data/saxs_computation/zk/9zkm/9zkm.fit
pddf	/app/data/pr_computation/zk/9zkm/9zkm.pr.out
profile	/app/data/saxs_computation/zk/9zkm/9zkm.dat

The LBD-TMD structure of native mouse AMPAR with 4 TARPs

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

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)