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9vsr

The DCY1040 and TUG-891-bound structure of TMEM175

Method: ELECTRON MICROSCOPY D_max: 94.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vsr
deposition_date	2025-07-09
title	The DCY1040 and TUG-891-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	28.37 Å
rg_electron	27.46 Å
i0	235815000.00
molecular_weight	86200.0 kDa
excluded_volume	85950 Å³
envelope_volume	145080 Å³
shell_volume	41868 Å³
envelope_diameter	100.5 Å
shell_rg	36.56 Å
envelope_rg	27.90 Å
shape_rg	27.50 Å
total_rg	28.07 Å
total_atoms	6562
n_residues	824
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	94.2 Å
rg_real	28.15 Å
rg_real_error	0.54 Å
i0_real	2.3580e+08
i0_real_error	3.5720e+06
rg_reciprocal	28.22 Å
i0_reciprocal	235800000.0000
total_estimate	0.8712
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.147
kurtosis	-0.358
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0001
highest_alpha	33350000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6594

MSQPRTPEQALDTPGDCPPGRRDEDAGEGIQCSQRMLSFSDALLSIIATVMILPVTHTEISPEQQFDRSVQRLLATRIAVYLMTFLIVTVAWAAHTRLFQVVGKTDDTLALLNLACMMTITFLPYTFSLMVTFPDVPLGIFLFCVCVIAIGVVQALIVGYAFHFPHLLSPQIQRSAHRALYRRHVLGIVLQGPALCFAAAIFSLFFVPLSYLLMVTVILLPYVSKVTGWCRDRLLGHREPSAHPVEVFSFDLHEPLSKERVEAFSDGVYAIVATLLILDICEDNVPDPKDVKERFSGSLVAALSATGPRFLAYFGSFATVGLLWFAHHSLFLHVRKATRAMGLLNTLSLAFVGGLPLAYQQTSAFARQPRDELERVRVSCTIIFLASIFQLAMWTTALLHQAETLQPSVWFGGREHVLMFAKLALYPCASLLAFASTCLLSRFSVGIFHLMQIAVPCAFLLLRLLVGLALATLRVLRGLARPEHPPPAPTGQDDPQSQLLPAPC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Mammalian expression vector EGFP-MCS-pcDNA3.1

Entity 2 non-polymer

description	;3-{4-[(4-fluoro-4'-methyl[1,1'-biphenyl]-2-yl)methoxy]phenyl}propanoic acid ;
formula_weight	364.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(2S)-2-butyl-2-cyclohexyl-6,7-bis(fluoranyl)-5-[3-(1H-1,2,3,4-tetrazol-5-yl)propoxy]-3H-inden-1-one
formula_weight	432.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	32

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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	2.92 Å
resolution_method	—
num_particles	249064

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