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

Method: ELECTRON MICROSCOPY D_max: 151.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zcq
deposition_date	2025-11-24
title	Avian TRPM8 (Parus major) semi-swapped, closed, calcium free, menthol bound structure resolved in cell vesicles
keywords	TRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, menthol; 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	52.57 Å
rg_electron	51.95 Å
i0	2509770000.00
molecular_weight	439860.0 kDa
excluded_volume	557790 Å³
envelope_volume	821500 Å³
shell_volume	126980 Å³
envelope_diameter	162.2 Å
shell_rg	60.16 Å
envelope_rg	49.80 Å
shape_rg	51.95 Å
total_rg	52.21 Å
total_atoms	61284
n_residues	3896
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	151.6 Å
rg_real	52.25 Å
rg_real_error	0.31 Å
i0_real	2.4220e+09
i0_real_error	3.5290e+07
rg_reciprocal	52.81 Å
i0_reciprocal	2512000000.0000
total_estimate	0.6778
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	70.8 Å
skewness	0.049
kurtosis	-0.515
angular_range	— – 0.1500 Å⁻¹
current_alpha	2.0720
highest_alpha	275400000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 0.915; Sysdev: 0.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.184

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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	61284

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	3.57 Å
resolution_method	—
num_particles	139033

fit	/app/data/saxs_computation/zc/9zcq/9zcq.fit
pddf	/app/data/pr_computation/zc/9zcq/9zcq.pr.out
profile	/app/data/saxs_computation/zc/9zcq/9zcq.dat