The DCY1020-bound structure of TMEM175

Method: ELECTRON MICROSCOPY D_max: 93.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vsp
deposition_date	2025-07-09
title	The DCY1020-bound structure of TMEM175
keywords	TMEM175, cro-EM, agonist, Parkinson, lysosome, 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	28.38 Å
rg_electron	27.46 Å
i0	232915000.00
molecular_weight	84598.0 kDa
excluded_volume	83788 Å³
envelope_volume	143470 Å³
shell_volume	41496 Å³
envelope_diameter	98.8 Å
shell_rg	36.42 Å
envelope_rg	27.88 Å
shape_rg	27.49 Å
total_rg	28.07 Å
total_atoms	6436
n_residues	820
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	93.8 Å
rg_real	28.17 Å
rg_real_error	0.66 Å
i0_real	2.3290e+08
i0_real_error	3.6650e+06
rg_reciprocal	28.23 Å
i0_reciprocal	232900000.0000
total_estimate	0.7975
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	36.8 Å
skewness	0.146
kurtosis	-0.362
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	32090000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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	3.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.40 Å
resolution_method	—
num_particles	50017

description	Endosomal/lysosomal proton channel TMEM175
formula_weight	55667.2 kDa
src_method	man
entity_count	2

The DCY1020-bound structure of TMEM175

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

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	Mammalian expression vector EGFP-MCS-pcDNA3.1

description	(2S)-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-5-[3-(1H-1,2,3,4-tetrazol-5-yl)propoxy]-3H-inden-1-one
formula_weight	451.4 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/vs/9vsp/9vsp.fit
pddf	/app/data/pr_computation/vs/9vsp/9vsp.pr.out
profile	/app/data/saxs_computation/vs/9vsp/9vsp.dat

type	polypeptide(L)
strand_id	A,B
atom_count	6436