Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4

Method: ELECTRON MICROSCOPY D_max: 80.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vpg
deposition_date	2025-07-03
title	Cryo-EM structure of human urate transporter GLUT9 bound to a selective inhibitor SG4
keywords	complex, selective inhibitor, transport protein; 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	24.28 Å
rg_electron	23.38 Å
i0	74146900.00
molecular_weight	47129.0 kDa
excluded_volume	46782 Å³
envelope_volume	78730 Å³
shell_volume	27911 Å³
envelope_diameter	82.1 Å
shell_rg	30.82 Å
envelope_rg	23.67 Å
shape_rg	23.38 Å
total_rg	24.08 Å
total_atoms	3596
n_residues	465
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	80.2 Å
rg_real	24.22 Å
rg_real_error	0.46 Å
i0_real	7.4150e+07
i0_real_error	9.3010e+05
rg_reciprocal	24.24 Å
i0_reciprocal	74150000.0000
total_estimate	0.8889
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	78.9 Å
skewness	0.300
kurtosis	-0.342
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	10420000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Solute carrier family 2, facilitated glucose transporter member 9
formula_weight	63215.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3596

MASWSHPQFEKGGGARGGSGGGSWSHPQFEKGFDYKDDDDKGTARKQNRNSKELGLVPLTDDTSHAGPPGPGRALLECDHLRSGVPGGRRRKDWSCSLLVASLAGAFGSSFLYGYNLSVVNAPTPYIKAFYNESWERRHGRPIDPDTLTLLWSVTVSIFAIGGLVGTLIVKMIGKVLGRKHTLLANNGFAISAALLMACSLQAGAFEMLIVGRFIMGIDGGVALSVLPMYLSEISPKEIRGSLGQVTAIFICIGVFTGQLLGLPELLGKESTWPYLFGVIVVPAVVQLLSLPFLPDSPRYLLLEKHNEARAVKAFQTFLGKADVSQEVEEVLAESRVQRSIRLVSVLELLRAPYVRWQVVTVIVTMACYQLCGLNAIWFYTNSIFGKAGIPPAKIPYVTLSTGGIETLAAVFSGLVIEHLGRRPLLIGGFGLMGLFFGTLTITLTLQDHAPWVPYLSIVGILAIIASFCSGPGGIPFILTGEFFQQSQRPAAFIIAGTVNWLSNFAVGLLFPFIQKSLDTYCFLVFATICITGAIYLYFVLPETKNRTYAEISQAFSKRNKAYPPEEKIDSAVTDGKINGRP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	(~{E})-3-[2-(4-hydroxyphenyl)-4-oxidanylidene-3~{H}-quinazolin-8-yl]-~{N}-propan-2-yl-prop-2-enamide
formula_weight	349.4 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	3.14 Å
resolution_method	—
num_particles	36474

fit	/app/data/saxs_computation/vp/9vpg/9vpg.fit
pddf	/app/data/pr_computation/vp/9vpg/9vpg.pr.out
profile	/app/data/saxs_computation/vp/9vpg/9vpg.dat