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12ag

Spermine-blocked open-state cryo-EM structure of human TRPV6 channel in cNW30 nanodiscs

Method: ELECTRON MICROSCOPY D_max: 146.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	12ag
deposition_date	2026-03-23
title	Spermine-blocked open-state cryo-EM structure of human TRPV6 channel in cNW30 nanodiscs
keywords	polyamine, spermine, cancer, cryo-EM, TRP channels, TRPV6, oncochannel, channel block, 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	47.66 Å
rg_electron	46.19 Å
i0	1056140000.00
molecular_weight	294620.0 kDa
excluded_volume	378970 Å³
envelope_volume	516370 Å³
shell_volume	89509 Å³
envelope_diameter	146.9 Å
shell_rg	54.30 Å
envelope_rg	45.03 Å
shape_rg	46.18 Å
total_rg	46.53 Å
total_atoms	20690
n_residues	2440
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	146.1 Å
rg_real	47.23 Å
rg_real_error	1.33 Å
i0_real	1.0560e+09
i0_real_error	2.0180e+07
rg_reciprocal	47.66 Å
i0_reciprocal	1057000000.0000
total_estimate	0.8911
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.4 Å
skewness	-0.049
kurtosis	-0.582
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	56920000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Transient receptor potential cation channel subfamily V member 6
formula_weight	70019.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	20694

ESWAQSRDEQNLLQQKRIWESPLLLAAKDNDVQALNKLLKYEDCKVHQRGAMGETALHIAALYDNLEAAMVLMEAAPELVFEPMTSELYEGQTALHIAVVNQNMNLVRALLARRASVSARATGTAFRRSPCNLIYFGEHPLSFAACVNSEEIVRLLIEHGADIRAQDSLGNTVLHILILQPNKTFACQMYNLLLSYDRHGDHLQPLDLVPNHQGLTPFKLAGVEGNTVMFQHLMQKRKHTQWTYGPLTSTLYDLTEIDSSGDEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWPRSGICGREYGLGDRWFLRVEDRQD

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	CHOLESTEROL HEMISUCCINATE
formula_weight	486.7 kDa
src_method	syn
entity_count	12

Entity 3 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	12

Entity 5 non-polymer

description	SPERMINE
formula_weight	202.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.48 Å
resolution_method	—
num_particles	14018

fit	/app/data/saxs_computation/2a/12ag/12ag.fit
pddf	/app/data/pr_computation/2a/12ag/12ag.pr.out
profile	/app/data/saxs_computation/2a/12ag/12ag.dat