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9rl5

a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin nanodiscs

Method: ELECTRON MICROSCOPY D_max: 127.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rl5
deposition_date	2025-06-16
title	a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin nanodiscs
keywords	GABAA receptor, pentameric ligand gated ion channel, ion channel, anticonvulsant, MEMBRANE PROTEIN; MEMBRANE 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	39.38 Å
rg_electron	38.92 Å
i0	639435000.00
molecular_weight	216030.0 kDa
excluded_volume	273760 Å³
envelope_volume	349520 Å³
shell_volume	72741 Å³
envelope_diameter	132.5 Å
shell_rg	46.52 Å
envelope_rg	38.42 Å
shape_rg	38.95 Å
total_rg	39.23 Å
total_atoms	15218
n_residues	1816
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	127.0 Å
rg_real	39.20 Å
rg_real_error	0.79 Å
i0_real	6.3940e+08
i0_real_error	1.0610e+07
rg_reciprocal	39.32 Å
i0_reciprocal	639500000.0000
total_estimate	0.8857
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.6 Å
skewness	0.243
kurtosis	-0.373
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	97430000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	Green fluorescent protein,Gamma-aminobutyric acid receptor subunit alpha-5,Gamma-aminobutyric acid receptor subunit alpha-5
formula_weight	76207.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	15218

MRKSPGLSDCLWAWILLLSTLTGRSYGQMSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATNGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGTYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFKIRHNVEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSVLSKDPNEKRDHMVLLEFVTAAGITHGMDELYKAANALAAWSHPQFEKGGGSGGGSGGGSWSHPQFEKSSSNNNNNENLYFQAMPTSSVKDETNDNITIFTRILDGLLDGYDNRLRPGLGERITQVRTDIYVTSFGPVSDTEMEYTIDVFFRQSWKDERLRFKGPMQRLPLNNLLASKIWTPDTFFHNGKKSIAHNMTTPNKLLRLEDDGTLLYTMRLTISAECPMQLEDFPMDAHACPLKFGSYAYPNSEVVYVWTNGSTKSVVVAEDGSRLNQYHLMGQTVGTENISTSTGEYTIMTAHFHLKRKIGYFVIQTYLPCIMTVILSQVSFWLNRESVPARTVFGVTTVLTMTTLSISARNSLPKVAYATAMDWFIAVCYAFVFSALIEFATVNYFTKSQPARAASISKIDKMSRIVFPVLFGTFNLVYWATYLNREPVIKGAASPK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Gamma-aminobutyric acid receptor subunit beta-3,Green fluorescent protein
formula_weight	71073.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	B,C,E

MWGLAGGRLFGIFSAPVLVAVVCCAQSVNDPGNMSFVKETVDKLLKGYDIRLRPDFGGPPVCVGMNIDIASIDMVSEVNMDYTLTMYFQQYWRDKRLAYSGIPLNLTLDNRVADQLWVPDTYFLNDKKSFVHGVTVKNRMIRLHPDGTVLYGLRITTTAACMMDLRRYPLDEQNCTLEIESYGYTTDDIEFYWRGGDKAVTGVERIELPQFSIVEHRLVSRNVVFATGAYPRLSLSFRLKRNIGYFILQTYMPSILITILSWVSFWINYDASAARVALGITTVLTMTTINTHLRETLPKIPYVKAIDMYLMGCFVFVFLALLEYAFVNYIFFSQPGRAMVSKGEELFTGVVPILVEMDGDVNGRKFSVRGVGEGDATHGKLTLKFICTSGKLPVPWPTLVTTLSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGSYKTRAEVKFEGDTLVNRIVLKGTDFKEDGNILGHKLEYNMNVGNVYITADKQKNGIKANFEIRHNVEDGGVQLADHYQQNTPIGDGSVLLPDNHYLSVQVKLSKDPNEKRDHMVLLEFRTAAGITPGMDELYKGRAAAIDRWSRIVFPFTFSLFNLVYWLYYVNSRENLYFQAHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Megabody 25
formula_weight	58275.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

MKKIWLALAGLVLAFSASAQVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKNTVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSSHHHHHHEPEA

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 4 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 5 branched

description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	3

Entity 6 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	2

Entity 7 branched

description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1073.0 kDa
src_method	man
entity_count	1

Entity 8 branched

description	beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	586.5 kDa
src_method	man
entity_count	1

Entity 9 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 10 non-polymer

description	GAMMA-AMINO-BUTANOIC ACID
formula_weight	103.1 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	;[(3aS,5aR,8aR,8bS)-2,2,7,7-tetramethyltetrahydro-3aH-bis[1,3]dioxolo[4,5-b:4',5'-d]pyran-3a-yl]methyl sulfamate ;
formula_weight	339.4 kDa
src_method	syn
entity_count	2

Entity 12 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 13 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
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	3.10 Å
resolution_method	—
num_particles	90532

fit	/app/data/saxs_computation/rl/9rl5/9rl5.fit
pddf	/app/data/pr_computation/rl/9rl5/9rl5.pr.out
profile	/app/data/saxs_computation/rl/9rl5/9rl5.dat

a5b3 GABAAR bound to Topiramate, GABA, and Mb25 in a desensitized state in saposin nanodiscs

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 (13)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 branched

Entity 6 branched

Entity 7 branched

Entity 8 branched

Entity 9 branched

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)