SAXSdb — 9qdn

▼

1. Structure Basics

entry_id	9qdn
deposition_date	2025-03-06
title	GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD
keywords	GRIA4, Calcium Voltage-Gated Channel Auxiliary Subunit Gamma 2, GluA4_TARP-2, NBQX, 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	45.32 Å
rg_electron	44.66 Å
i0	887711000.00
molecular_weight	266430.0 kDa
excluded_volume	341440 Å³
envelope_volume	472290 Å³
shell_volume	85432 Å³
envelope_diameter	142.9 Å
shell_rg	51.65 Å
envelope_rg	43.83 Å
shape_rg	44.65 Å
total_rg	45.01 Å
total_atoms	18760
n_residues	2360
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	146.2 Å
rg_real	45.09 Å
rg_real_error	1.29 Å
i0_real	8.8770e+08
i0_real_error	1.6520e+07
rg_reciprocal	45.31 Å
i0_reciprocal	887900000.0000
total_estimate	0.8916
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	54.3 Å
skewness	0.156
kurtosis	-0.480
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	82270000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.914

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Voltage-dependent calcium channel gamma-2 subunit
formula_weight	35950.8 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	H,G,E,F
atom_count	18807

MGLFDRGVQMLLTIVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSSSRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVHNCIQKDSKDSLHANTANRRTTPV

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 2 polymer

description	Isoform 2 of Glutamate receptor 4
formula_weight	98671.9 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,A,C,B

GAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTNAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPSLRGALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWHVSAICVENFNDVSYRQLLEELDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFIHGGANVTGFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSALTYDGVLVMAETFRSLRRQKIDISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVFELKSTGPRKVGYWNDMDKLVLIQDMPTLGNDTAAIENRTVVVTTIMESPYVMYKKNHEMFEGNDKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEAGVLDKLKNKWWYDKGECGPKDSGSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKLTFSEATRNKARLSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASDLP

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Homo sapiens

Entity 3 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	syn
entity_count	16

Entity 4 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
formula_weight	336.3 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	15

▶

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	—

resolution	2.71 Å
resolution_method	—
num_particles	296802

fit	/app/data/saxs_computation/qd/9qdn/9qdn.fit
pddf	/app/data/pr_computation/qd/9qdn/9qdn.pr.out
profile	/app/data/saxs_computation/qd/9qdn/9qdn.dat

GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)