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9w97

Structure of BPDBA-bound state of the human betaine/GABA transporter 1

Method: ELECTRON MICROSCOPY D_max: 83.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w97
deposition_date	2025-08-09
title	Structure of BPDBA-bound state of the human betaine/GABA transporter 1
keywords	TRANSPORT PROTEIN, 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	24.42 Å
rg_electron	23.51 Å
i0	104309000.00
molecular_weight	57587.0 kDa
excluded_volume	57802 Å³
envelope_volume	89135 Å³
shell_volume	30730 Å³
envelope_diameter	87.8 Å
shell_rg	31.55 Å
envelope_rg	23.99 Å
shape_rg	23.50 Å
total_rg	24.20 Å
total_atoms	4397
n_residues	540
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	83.7 Å
rg_real	24.38 Å
rg_real_error	0.45 Å
i0_real	1.0430e+08
i0_real_error	1.2340e+06
rg_reciprocal	24.39 Å
i0_reciprocal	104300000.0000
total_estimate	0.8626
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.2 Å
skewness	0.392
kurtosis	-0.109
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	18510000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.750; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.979

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	GFP,Maltose/maltodextrin-binding periplasmic protein,Sodium- and chloride-dependent betaine transporter
formula_weight	144419.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4397

MSKGEELFTGVVPILVELDGDVNGHKFSVRGEGEGDATIGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGKYKTRAVVKFEGDTLVNRIELKGTDFKEDGNILGHKLEYNFNSHNVYITADKQKNGIKANFTVRHNVEGSGHHHHHHHHADRKAAVSHWQQSSGLVPRGSGWSHPQFEKGSGDYKDDDDKGSGWSHPQFEKGSGDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQTKLSKDPNEKRDHMVLHEYVNAAGITGSMKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYENGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSKVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELVKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDEALKDAQTGGLEVLFQGPEFMDGKVAVQERGPPAVSWVPEEGEKLDQEDEDQVKDRGQWTNKMEFVLSVAGEIIGLGNVWRFPYLCYKNGGGAFFIPYFIFFFVCGIPVFFLEVALGQYTSQGSVTAWRKICPLFQGIGLASVVIESYLNVYYIIILAWALFYLFSSFTSELPWTTCNNFWNTEHCTDFLNHSGAGTVTPFENFTSPVMEFWERRVLGITSGIHDLGSLRWELALCLLLAWVICYFCIWKGVKSTGKVVYFTATFPYLMLVILLIRGVTLPGAYQGIIYYLKPDLFRLKDPQVWMDAGTQIFFSFAICQGCLTALGSYNKYHNNCYKDCIALCFLNSATSFVAGFVVFSILGFMSQEQGVPISEVAESGPGLAFIAFPKAVTMMPLSQLWSCLFFIMLIFLGLDSQFVCVECLVTASIDMFPRQLRKSGRRELLILTIAVMCYLIGLFLVTEGGMYIFQLFDYYASSGICLLFLSLFEVVCISWVYGADRFYDNIEDMIGYRPWPLVKISWLFLTPGLCLATFLFSLSKYTPLKYNNVYVYPPWGYSIGWFLALSSMVCVPLFVVITLLKTRGPFRKRLRQLITPDSSLPQPKQHPCLDGSAGRNFGPSPTREGLIAGEKETHL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	2,4-bis(chloranyl)-~{N}-[1-(phenylmethyl)piperidin-4-yl]benzamide
formula_weight	363.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 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	2.840 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.84 Å
resolution_method	—
num_particles	92959

fit	/app/data/saxs_computation/w9/9w97/9w97.fit
pddf	/app/data/pr_computation/w9/9w97/9w97.pr.out
profile	/app/data/saxs_computation/w9/9w97/9w97.dat

Structure of BPDBA-bound state of the human betaine/GABA transporter 1

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