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9uvz

Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425

Method: ELECTRON MICROSCOPY D_max: 122.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uvz
deposition_date	2025-05-11
title	Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
keywords	GPCR, LPA2, Lysophosphatidic acid receptor 2, Ki16425, ARK1, 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	34.81 Å
rg_electron	35.07 Å
i0	179163000.00
molecular_weight	72084.0 kDa
excluded_volume	69820 Å³
envelope_volume	124080 Å³
shell_volume	32240 Å³
envelope_diameter	122.2 Å
shell_rg	37.67 Å
envelope_rg	35.22 Å
shape_rg	35.02 Å
total_rg	35.31 Å
total_atoms	5474
n_residues	682
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	122.3 Å
rg_real	35.17 Å
rg_real_error	1.22 Å
i0_real	1.7920e+08
i0_real_error	2.8410e+06
rg_reciprocal	34.94 Å
i0_reciprocal	179100000.0000
total_estimate	0.6194
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	29.9 Å
skewness	0.547
kurtosis	-0.395
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	19870000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.601; Smooth: 0.860

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lysophosphatidic acid receptor 2,ARK1
formula_weight	86158.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5487

MKTIIALSYIFCLVFADYKDDDDAENLYFQGMGQCYYNETIGFFYNNSGKELSSHWRPKDVVVVALGLTVSVLVLLTNLLVIAAIASNRRFHQPIYYLLGNLAAADLFAGVAYLFLMFHTGPRTARLSLEGWFLRQGLLDTSLTASVATLLAIAVERHRSVMAVQLHSRLPRGRVVMLIVGVWVAALGLGLLPAHSWHCLCALDRCSRMAPLLSRSYLAVWALSSLLVFLLMVAVYTRIFFYVRRRVQRMLELRRLLREQGEKLLKLAEESEKKIKEAIEKGEDVVKVATEETHKLIKAIWESSFEVARLLGVPEEVLEKFRKELEKLLEESKKRIEEAIKKGEDVLKVVEEEAKKLREHSEKFLETARSLGVDPRPLERLARIVRVVEESLVRIVKAIKEGEDVEKVLLSESTLIKSSIILSSGLDPREAYEELLATYEETRDSELVKEFVELVRELLRLRGEPEELVRQLDKLIEAIDRMEKAVAEGEDTLPLFLELAREILKALSDVARILAEREGLDVELIDEIVDTASRLLEEVIKKAKEGEDLDEEEEKVKKELEELKKRTEERARALGQDVELVRTIVDSLSTLLSEIVEGIKRVKEGEDPLEVLARVVLTATLQILELVRTAERRRRERTLSLVKTVVIILGAFVVCWTPGQVVLLLDGLGCESCNVLAVEKYFLLLAEANSLVNAAVYSCRDAEMRRTFRRLLCCACLRQSTRESVHYTSSAQGGASTRIMLPENGHPLMDSTLLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid
formula_weight	475.0 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	4

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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	2.990 Å
resolution_low	2.990 Å
r_factor	—
r_work	0.3988
r_free	—

resolution	2.99 Å
resolution_method	—
num_particles	151855

fit	/app/data/saxs_computation/uv/9uvz/9uvz.fit
pddf	/app/data/pr_computation/uv/9uvz/9uvz.pr.out
profile	/app/data/saxs_computation/uv/9uvz/9uvz.dat

Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425

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