Cryo-EM structure of TMEM63A-digitonin-cholesterol

Method: ELECTRON MICROSCOPY D_max: 100.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wxv
deposition_date	2025-09-26
title	Cryo-EM structure of TMEM63A-digitonin-cholesterol
keywords	ion channels, lipid scramblase, 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	31.62 Å
rg_electron	30.28 Å
i0	70746200.00
molecular_weight	72941.0 kDa
excluded_volume	94133 Å³
envelope_volume	125160 Å³
shell_volume	35384 Å³
envelope_diameter	102.2 Å
shell_rg	36.50 Å
envelope_rg	30.42 Å
shape_rg	30.25 Å
total_rg	31.07 Å
total_atoms	5152
n_residues	626
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	100.9 Å
rg_real	31.67 Å
rg_real_error	0.77 Å
i0_real	7.0750e+07
i0_real_error	1.1620e+06
rg_reciprocal	31.65 Å
i0_reciprocal	70750000.0000
total_estimate	0.7039
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.3 Å
skewness	0.303
kurtosis	-0.551
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	6886000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.955; Stabil: 1.000; Sysdev: 0.169; Positv: 1.000; Valcen: 0.981; Smooth: 0.793

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Mechanosensitive cation channel TMEM63A
formula_weight	92743.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5152

MMDSPFLELWQSKAVSIREQLGLGDRPNDSYCYNSAKNSTVLQGVTFGGIPTVLLIDVSCFLFLILVFSIIRRRFWDYGRIALVSEADSESRFQRLSSTSSSGQQDFENELGCCPWLTAIFRLHDDQILEWCGEDAIHYLSFQRHIIFLLVVVSFLSLCVILPVNLSGDLLDKDPYSFGRTTIANLQTDNDLLWLHTIFAVIYLFLTVGFMRHHTQSIKYKEENLVRRTLFITGLPRDARKETVESHFRDAYPTCEVVDVQLCYNVAKLIYLCKEKKKTEKSLTYYTNLQVKTGQRTLINPKPCGQFCCCEVLGCEWEDAISYYTRMKDRLLERITEEERHVQDQPLGMAFVTFQEKSMATYILKDFNACKCQSLQCKGEPQPSSHSRELYTSKWTVTFAADPEDICWKNLSIQGLRWWLQWLGINFTLFLGLFFLTTPSIILSTMDKFNVTKPIHALNNPIISQFFPTLLLWSFSALLPSIVYYSTLLESHWTKSGENQIMMTKVYIFLIFMVLILPSLGLTSLDFFFRWLFDKTSSEASIRLECVFLPDQGAFFVNYVIASAFIGNGMELLRLPGLILYTFRMIMAKTAADRRNVKQNQAFQYEFGAMYAWMLCVFTVIVAYSITCPIIAPFGLIYILLKHMVDRHNLYFVYLPAKLEKGIHFAAVNQALAAPILCLFWLYFFSFLRLGMKAPATLFTFLVLLLTILVCLAHTCFGCFKHLSPLNYKTEEPASDKGSEAEAHMPPPFTPYVPRILNGLASERTALSPQQQQQQTYGAIHNISGTIPGQCLAQSATGSVAAAPQEASNSLE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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resolution	4.400 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.40 Å
resolution_method	—
num_particles	202829

fit	/app/data/saxs_computation/wx/9wxv/9wxv.fit
pddf	/app/data/pr_computation/wx/9wxv/9wxv.pr.out
profile	/app/data/saxs_computation/wx/9wxv/9wxv.dat