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9zq0

CNGA1 channel closed state in nanodisc with diC8-PIP2 cGMP-free

Method: ELECTRON MICROSCOPY D_max: 125.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zq0
deposition_date	2025-12-17
title	CNGA1 channel closed state in nanodisc with diC8-PIP2 cGMP-free
keywords	Cyclic nucleotide-gated channel, Rod photoreceptor, CNGA1, Ion channel, 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	40.47 Å
rg_electron	39.83 Å
i0	623271000.00
molecular_weight	229700.0 kDa
excluded_volume	297640 Å³
envelope_volume	380070 Å³
shell_volume	76282 Å³
envelope_diameter	123.2 Å
shell_rg	48.22 Å
envelope_rg	39.12 Å
shape_rg	39.83 Å
total_rg	40.30 Å
total_atoms	16138
n_residues	1800
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	125.5 Å
rg_real	40.27 Å
rg_real_error	1.03 Å
i0_real	6.2330e+08
i0_real_error	1.1310e+07
rg_reciprocal	40.47 Å
i0_reciprocal	623400000.0000
total_estimate	0.8881
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	51.5 Å
skewness	0.134
kurtosis	-0.449
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	56410000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.915

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Cyclic nucleotide-gated channel alpha-1
formula_weight	64519.2 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16138

DYKDDDDKGGSASKDKKEEEKKEVVVIDPSGNTYYNWLFCITLPVMYNWTMVIARACFDELQSDYLEYWLILDYVSDIVYLIDMFVRTRTGYLEQGLLVKEELKLINKYKSNLQFKLDVLSLIPTDLLYFKLGWNYPEIRLNRLLRFSRMFEFFQRTETRTNYPNIFRISNLVMYIVIIIHWNACVFYSISKAIGFGNDTWVYPDINDPEFGRLARKYVYSLYWSTLTLTTIGETPPPVRDSEYVFVVVDFLIGVLIFATIVGNIGSMISNMNAARAEFQARIDAIKQYMHFRNVSKDMEKRVIKWFDYLWTNKKTVDEKEVLKYLPDKLRAEIAINVHLDTLKKVRIFADCEAGLLVELVLKLQPQVYSPGDYICKKGDIGREMYIIKEGKLAVVADDGVTQFVVLSDGSYFGEISILNIKGSKAGNRRTANIKSIGYSDLFCLSKDDLMEALTEYPDAKTMLEEKGKQILMKDGLLDLNIANAGSDPKDLEEKVTRMEGSVDLLQTRFARILAEYESMQQKLKQRLTKVEKFLKPLIDTEFSSIEGPGAESGPIDST

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
formula_weight	787.1 kDa
src_method	syn
entity_count	28

Entity 4 non-polymer

description	;[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate ;
formula_weight	746.6 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	5

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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	2.110 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.11 Å
resolution_method	—
num_particles	504391

fit	/app/data/saxs_computation/zq/9zq0/9zq0.fit
pddf	/app/data/pr_computation/zq/9zq0/9zq0.pr.out
profile	/app/data/saxs_computation/zq/9zq0/9zq0.dat