Cryo-EM structure of human OAT1 in complex with probenecid

Method: ELECTRON MICROSCOPY D_max: 94.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u55
deposition_date	2025-03-20
title	Cryo-EM structure of human OAT1 in complex with probenecid
keywords	transporter, OAT1, organic anion transport, 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	25.75 Å
rg_electron	24.98 Å
i0	41317600.00
molecular_weight	52683.0 kDa
excluded_volume	67084 Å³
envelope_volume	79106 Å³
shell_volume	27365 Å³
envelope_diameter	99.4 Å
shell_rg	31.30 Å
envelope_rg	25.56 Å
shape_rg	25.03 Å
total_rg	25.55 Å
total_atoms	3707
n_residues	496
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	94.7 Å
rg_real	25.90 Å
rg_real_error	0.96 Å
i0_real	4.1320e+07
i0_real_error	6.3570e+05
rg_reciprocal	25.85 Å
i0_reciprocal	41320000.0000
total_estimate	0.8272
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.5 Å
skewness	0.590
kurtosis	0.158
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	7867000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.851; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (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	3.17 Å
resolution_method	—
num_particles	82328

description	Isoform 2 of Solute carrier family 22 member 6
formula_weight	63119.2 kDa
src_method	man
entity_count	1

type	polypeptide(L)
strand_id	A
atom_count	3707

Cryo-EM structure of human OAT1 in complex with probenecid

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

description	4-(dipropylsulfamoyl)benzoic acid
formula_weight	285.4 kDa
src_method	syn
entity_count	1

fit	/app/data/saxs_computation/u5/9u55/9u55.fit
pddf	/app/data/pr_computation/u5/9u55/9u55.pr.out
profile	/app/data/saxs_computation/u5/9u55/9u55.dat