Human TRPM8 V915Y fully-swapped, closed, ligand-free structure resolved in GDN

Method: ELECTRON MICROSCOPY D_max: 165.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zcu
deposition_date	2025-11-24
title	Human TRPM8 V915Y fully-swapped, closed, ligand-free structure resolved in GDN
keywords	TRPM8, transient receptor potential melastatin 8, 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	52.49 Å
rg_electron	51.96 Å
i0	2232210000.00
molecular_weight	420880.0 kDa
excluded_volume	536070 Å³
envelope_volume	785040 Å³
shell_volume	122060 Å³
envelope_diameter	170.5 Å
shell_rg	59.38 Å
envelope_rg	50.17 Å
shape_rg	52.02 Å
total_rg	51.94 Å
total_atoms	58152
n_residues	3884
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	165.3 Å
rg_real	52.20 Å
rg_real_error	1.22 Å
i0_real	2.2320e+09
i0_real_error	4.2550e+07
rg_reciprocal	52.71 Å
i0_reciprocal	2234000000.0000
total_estimate	0.8803
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	71.6 Å
skewness	0.075
kurtosis	-0.460
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	257300000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.856

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Transient receptor potential cation channel subfamily M member 8
formula_weight	128398.2 kDa
mutation	V915Y
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	58152

GPGSGSGMSFRAARLSMRNRRNDTLDSTRTLYSSASRSTDLSYSESDLVNFIQANFKKRECVFFTKDSKATENVCKCGYAQSQHMEGTQINQSEKWNYKKHTKEFPTDAFGDIQFETLGKKGKYIRLSCDTDAEILYELLTQHWHLKTPNLVISVTGGAKNFALKPRMRKIFSRLIYIAQSKGAWILTGGTHYGLMKYIGEVVRDNTISRSSEENIVAIGIAAWGMVSNRDTLIRNCDAEGYFLAQYLMDDFTRDPLYILDNNHTHLLLVDNGCHGHPTVEAKLRNQLEKYISERTIQDSNYGGKIPIVCFAQGGGKETLKAINTSIKNKIPCVVVEGSGQIADVIASLVEVEDALTSSAVKEKLVRFLPRTVSRLPEEETESWIKWLKEILECSHLLTVIKMEEAGDEIVSNAISYALYKAFSTSEQDKDNWNGQLKLLLEWNQLDLANDEIFTNDRRWESADLQEVMFTALIKDRPKFVRLFLENGLNLRKFLTHDVLTELFSNHFSTLVYRNLQIAKNSYNDALLTFVWKLVANFRRGFRKEDRNGRDEMDIELHDVSPITRHPLQALFIWAILQNKKELSKVIWEQTRGCTLAALGASKLLKTLAKVKNDINAAGESEELANEYETRAVELFTECYSSDEDLAEQLLVYSCEAWGGSNCLELAVEATDQHFIAQPGVQNFLSKQWYGEISRDTKNWKIILCLFIIPLVGCGFVSFRKKPVDKHKKLLWYYVAFFTSPFVVFSWNVVFYIAFLLLFAYVLLMDFHSVPHPPELVLYSLVFVLFCDEVRQWYVNGVNYFTDLWNVMDTLGLFYFIAGIVFRLHSSNKSSLYSGRVIFCLDYIIFTLRLIHIFTVSRNLGPKIIMLQRMLIDVFFFLFLFAVWMVAFGVARQGILRQNEQRWRWIFRSVIYEPYLAMFGQYPSDVDGTTYDFAHCTFTGNESKPLCVELDEHNLPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGTVQENNDQVWKFQRYFLVQEYCSRLNIPFPFIVFAYFYMVVKKCFKCCCKEKNMESSVCCFKNEDNETLAWEGVMKENYLVKINTKANDTSEEMRHRFRQLDTKLNDLKGLLKEIANKIK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	2.86 Å
resolution_method	—
num_particles	96564

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

Human TRPM8 V915Y fully-swapped, closed, ligand-free structure resolved in GDN

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

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)