Avian TRPM8 (Parus major) semi-swapped, closed, ligand-free in the presence of calcium, structure resolved in cell vesicles

Method: ELECTRON MICROSCOPY D_max: 167.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zco
deposition_date	2025-11-24
title	Avian TRPM8 (Parus major) semi-swapped, closed, ligand-free in the presence of calcium, structure resolved in cell vesicles
keywords	TRPM8, transient receptor potential melastatin 8, MEMBRANE PROTEIN, Parus major; 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	53.61 Å
rg_electron	52.97 Å
i0	2502580000.00
molecular_weight	439470.0 kDa
excluded_volume	557340 Å³
envelope_volume	851680 Å³
shell_volume	129410 Å³
envelope_diameter	163.9 Å
shell_rg	61.21 Å
envelope_rg	50.52 Å
shape_rg	52.97 Å
total_rg	53.24 Å
total_atoms	61240
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	167.5 Å
rg_real	53.28 Å
rg_real_error	0.81 Å
i0_real	2.5030e+09
i0_real_error	4.7760e+07
rg_reciprocal	53.88 Å
i0_reciprocal	2505000000.0000
total_estimate	0.8858
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	69.3 Å
skewness	0.021
kurtosis	-0.539
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0001
highest_alpha	289800000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; 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	61240

GPGSGSGMRHRRNGNFESSRLLYSSMSRSIDVACSDADLANFIQENFKKRECVFFTKDTKSMGNLCKCGYPENQHIEGTQVNTTEKWNYKKHTKELPTDAFGDIQFENLGKRGKYIRLSCDTDSETLYDLMTQHWHLKTPNLVISVTGGAKNFALKPRMRKIFSRLIYIAQSKGAWIFTGGTHYGLMKYIGEVVRDNTISRSSEENVVAIGIAAWGMISNRETLIRTADSDGSFLARYIMDDLKRDPLYCLDNNHTHLLLVDNGTHGHPTTEAKVRTQLEKYISERVIPESNYGGKIPIVCFAQGGGKETLKSINVAIKSKIPCVVVEGSGRIADVIASLVEAEGTLASSCVKESLLRFLPRTISRLSEEETESWIKWIKEVLESPHLLTVIKIEEAGDEIVSNAISFALYKAFSTNEHDRDNWNGQLKLLLEWNQLDLASDEIFTNDRNWESADLQDVMFTALVKDRPKFVRLFLENGLNLRKFLTTEVLRELYTNNFSSLVFKNLQIAKNSYNDALLTFVWKMVEDFRRGFKRDYKNSKDEMEIQLSEECPITRHPLQALFIWSVLQNKKELSKVIWEQTRGCTLAALGASKLLKSMAKVKNDINAAGESEELANEYETRAVELFTECYSNDEDLAEQLLTYSCEAWGGSNCLELAVEARDQQFIAQPGVQNFLSKQWYGEISRDTKNWKIIMCLFFFPLIGCGFISFRKKPVEKSKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFVLLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDRCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRLTIPFPFVIFAYIFMVMRKCFKCCCNKESKEPSICCSRNEDNEILAWEAVMKENYLVKINTKANDSSEEMVHRFRQLDAKLSDLKGLLKEISSKIK

Source

organism	Parus major
common_name	Great Tit
ncbi_taxonomy_id	9157
host_organism	Homo sapiens

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 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	3.45 Å
resolution_method	—
num_particles	61895

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