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9wml

Structural mechanism of substrate binding of the human Proline Transporter

Method: ELECTRON MICROSCOPY D_max: 83.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wml
deposition_date	2025-09-03
title	Structural mechanism of substrate binding of the human Proline Transporter
keywords	TRANSPORT PROTEIN, L-PROLINE; TRANSPORT 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	24.77 Å
rg_electron	23.46 Å
i0	48465100.00
molecular_weight	62844.0 kDa
excluded_volume	82169 Å³
envelope_volume	89538 Å³
shell_volume	30934 Å³
envelope_diameter	85.1 Å
shell_rg	31.63 Å
envelope_rg	23.79 Å
shape_rg	23.47 Å
total_rg	24.43 Å
total_atoms	4438
n_residues	541
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	83.3 Å
rg_real	24.75 Å
rg_real_error	0.58 Å
i0_real	4.8470e+07
i0_real_error	7.1940e+05
rg_reciprocal	24.75 Å
i0_reciprocal	48470000.0000
total_estimate	0.6867
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.1 Å
skewness	0.386
kurtosis	-0.203
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	9121000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 0.184; Positv: 1.000; Valcen: 0.982; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Sodium-dependent proline transporter
formula_weight	70960.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4438

MKKLQGAHLRKPVTPDLLMTPSDQGDVDLDVDFAAHRGNWTGKLDFLLSCIGYCVGLGNVWRFPYRAYTNGGGAFLVPYFLMLAICGIPLFFLELSLGQFSSLGPLAVWKISPLFKGAGAAMLLIVGLVAIYYNMIIAYVLFYLFASLTSDLPWEHCGNWWNTELCLEHRVSKDGNGALPLNLTCTVSPSEEYWSRYVLHIQGSQGIGSPGEIRWNLCLCLLLAWVIVFLCILKGVKSSGKVVYFTATFPYLILLMLLVRGVTLPGAWKGIQFYLTPQFHHLLSSKVWIEAALQIFYSLGVGFGGLLTFASYNTFHQNIYRDTFIVTLGNAITSILAGFAIFSVLGYMSQELGVPVDQVAKAGPGLAFVVYPQAMTMLPLSPFWSFLFFFMLLTLGLDSQFAFLETIVTAVTDEFPYYLRPKKAVFSGLICVAMYLMGLILTTDGGMYWLVLLDDYSASFGLMVVVITTCLAVTRVYGIQRFCRDIHMMLGFKPGLYFRACWLFLSPATLLALMVYSIVKYQPSEYGSYRFPPWAELLGILMGLLSCLMIPAGMLVAVLREEGSLWERLQQASRPAMDWGPSLEENRTGMYVATLAGSQSPKPLMVHMRKYGGITSFENTAIEVDREIAEEEESMM

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(2S)-2,3-dihydro-1H-pyrrole-2-carboxylic acid
formula_weight	113.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 kDa
src_method	syn
entity_count	2

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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	2.79 Å
resolution_method	—
num_particles	144216

fit	/app/data/saxs_computation/wm/9wml/9wml.fit
pddf	/app/data/pr_computation/wm/9wml/9wml.pr.out
profile	/app/data/saxs_computation/wm/9wml/9wml.dat