Avian TRPM8 (Parus major) semi-swapped, calcium free, menthol bound structure resolved in cell vesicles

Method: ELECTRON MICROSCOPY D_max: 159.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zez
deposition_date	2025-12-01
title	Avian TRPM8 (Parus major) semi-swapped, calcium free, menthol bound structure resolved in cell vesicles
keywords	TRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, menthol, TRANSPORT PROTEIN; TRANSPORT 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	51.18 Å
rg_electron	50.91 Å
i0	2160720000.00
molecular_weight	410480.0 kDa
excluded_volume	521780 Å³
envelope_volume	765640 Å³
shell_volume	121130 Å³
envelope_diameter	162.0 Å
shell_rg	58.98 Å
envelope_rg	48.78 Å
shape_rg	50.93 Å
total_rg	51.10 Å
total_atoms	57384
n_residues	3632
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	159.9 Å
rg_real	50.89 Å
rg_real_error	0.92 Å
i0_real	2.1610e+09
i0_real_error	3.7940e+07
rg_reciprocal	51.41 Å
i0_reciprocal	2162000000.0000
total_estimate	0.8847
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.1 Å
skewness	0.034
kurtosis	-0.496
angular_range	— – 0.1550 Å⁻¹
current_alpha	0.0000
highest_alpha	294900000.0000
n_real_points	32
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.904

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Transient receptor potential cation channel subfamily M member 8
formula_weight	127217.0 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	57384

GPGSGSGMRHRRNGNFESSRLLYSSMSRSIDVACSDADLANFIQENFKKRECVFFTKDTKSMGNLCKCGYPENQHIEGTQVNTTEKWNYKKHTKELPTDAFGDIQFENLGKRGKYIRLSCDTDSETLYDLMTQHWHLKTPNLVISVTGGAKNFALKPRMRKIFSRLIYIAQSKGAWIFTGGTHYGLMKYIGEVVRDNTISRSSEENVVAIGIAAWGMISNRETLIRTADSDGSFLARYIMDDLKRDPLYCLDNNHTHLLLVDNGTHGHPTTEAKVRTQLEKYISERVIPESNYGGKIPIVCFAQGGGKETLKSINVAIKSKIPCVVVEGSGRIADVIASLVEAEGTLASSCVKESLLRFLPRTISRLSEEETESWIKWIKEVLESPHLLTVIKIEEAGDEIVSNAISFALYKAFSTNEHDRDNWNGQLKLLLEWNQLDLASDEIFTNDRNWESADLQDVMFTALVKDRPKFVRLFLENGLNLRKFLTTEVLRELYTNNFSSLVFKNLQIAKNSYNDALLTFVWKMVEDFRRGFKRDYKNSKDEMEIQLSEECPITRHPLQALFIWSVLQNKKELSKVIWEQTRGCTLAALGASKLLKSMAKVKNDINAAGESEELANEYETRAVELFTECYSNDEDLAEQLLTYSCEAWGGSNCLELAVEARDQQFIAQPGVQNFLSKQWYGEISRDTKNWKIIMCLFFFPLIGCGFISFRKKPVEKSKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFVLLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDRCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRLTIPFPFVIFAYIFMVMRKCFKCCCNKESKEPSICCSRNEDNEILAWEAVMKENYLVKINTKANDSSEEMVHRFRQLDAKLSDLKGLLKEISSKIK

Source

organism	Parus major
common_name	Great Tit
ncbi_taxonomy_id	9157
host_organism	Homo sapiens

Entity 2 non-polymer

description	(1R,2S,5R)-5-methyl-2-(propan-2-yl)cyclohexan-1-ol
formula_weight	156.3 kDa
src_method	syn
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	3.41 Å
resolution_method	—
num_particles	541958

fit	/app/data/saxs_computation/ze/9zez/9zez.fit
pddf	/app/data/pr_computation/ze/9zez/9zez.pr.out
profile	/app/data/saxs_computation/ze/9zez/9zez.dat