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9ued

Cryo-EM structure of human TRPV3 in complex with sevoflurane determined in MSP2N2 nanodisc

Method: ELECTRON MICROSCOPY D_max: 144.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ued
deposition_date	2025-04-08
title	Cryo-EM structure of human TRPV3 in complex with sevoflurane determined in MSP2N2 nanodisc
keywords	Transient Receptor Potential Vanilloid 3, 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	47.24 Å
rg_electron	46.57 Å
i0	2113360000.00
molecular_weight	263650.0 kDa
excluded_volume	260170 Å³
envelope_volume	508880 Å³
shell_volume	87642 Å³
envelope_diameter	145.8 Å
shell_rg	54.65 Å
envelope_rg	45.31 Å
shape_rg	46.55 Å
total_rg	46.85 Å
total_atoms	20020
n_residues	2408
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	144.2 Å
rg_real	46.83 Å
rg_real_error	1.22 Å
i0_real	2.1130e+09
i0_real_error	3.7370e+07
rg_reciprocal	47.24 Å
i0_reciprocal	2114000000.0000
total_estimate	0.8845
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	-0.019
kurtosis	-0.514
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	57090000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.837

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Transient receptor potential cation channel subfamily V member 3
formula_weight	91960.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	20020

MKAHPKEMVPLMGKRVAAPSGNPAVLPEKRPAEITPTKKSAHFFLEIEGFEPNPTVAKTSPPVFSKPMDSNIRQCISGNCDDMDSPQSPQDDVTETPSNPNSPSAQLAKEEQRRKKRRLKKRIFAAVSEGCVEELVELLVELQELCRRRHDEDVPDFLMHKLTASDTGKTCLMKALLNINPNTKEIVRILLAFAEENDILGRFINAEYTEEAYEGQTALNIAIERRQGDIAALLIAAGADVNAHAKGAFFNPKYQHEGFYFGETPLALAACTNQPEIVQLLMEHEQTDITSRDSRGNNILHALVTVAEDFKTQNDFVKRMYDMILLRSGNWELETTRNNDGLTPLQLAAKMGKAEILKYILSREIKEKRLRSLSRKFTDWAYGPVSSSLYDLTNVDTTTDNSVLEITVYNTNIDNRHEMLTLEPLHTLLHMKWKKFAKHMFFLSFCFYFFYNITLTLVSYYRPREEEAIPHPLALTHKMGWLQLLGRMFVLIWAMCISVKEGIAIFLLRPSDLQSILSDAWFHFVFFIQAVLVILSVFLYLFAYKEYLACLVLAMALGWANMLYYTRGFQSMGMYSVMIQKVILHDVLKFLFVYIVFLLGFGVALASLIEKCPKDNKDCSSYGSFSDAVLELFKLTIGLGDLNIQQNSKYPILFLFLLITYVILTFVLLLNMLIALMGETVENVSKESERIWRLQRARTILEFEKMLPEWLRSRFRMGELCKVAEDDFRLCLRINEVKWTEWKTHVSFLNEDPGPVRRTDFNKIQDSSRNNSKTTLNAFEEVEEFPETSVAAASNSLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	sevoflurane
formula_weight	200.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	8

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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	3.290 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.29 Å
resolution_method	—
num_particles	38843

fit	/app/data/saxs_computation/ue/9ued/9ued.fit
pddf	/app/data/pr_computation/ue/9ued/9ued.pr.out
profile	/app/data/saxs_computation/ue/9ued/9ued.dat

Cryo-EM structure of human TRPV3 in complex with sevoflurane determined in MSP2N2 nanodisc

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