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9zpy

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

Method: ELECTRON MICROSCOPY D_max: 123.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zpy
deposition_date	2025-12-17
title	CNGA1 channel closed state in nanodisc with brain 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	40.53 Å
rg_electron	39.84 Å
i0	612370000.00
molecular_weight	228250.0 kDa
excluded_volume	295980 Å³
envelope_volume	378010 Å³
shell_volume	75951 Å³
envelope_diameter	123.1 Å
shell_rg	48.16 Å
envelope_rg	39.06 Å
shape_rg	39.84 Å
total_rg	40.34 Å
total_atoms	16048
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	123.8 Å
rg_real	40.33 Å
rg_real_error	0.67 Å
i0_real	6.1240e+08
i0_real_error	9.1940e+06
rg_reciprocal	40.53 Å
i0_reciprocal	612500000.0000
total_estimate	0.8870
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.8 Å
skewness	0.125
kurtosis	-0.463
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	52620000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.827

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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	16048

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	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	;[(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate ;
formula_weight	1047.1 kDa
src_method	syn
entity_count	2

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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	2.480 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.48 Å
resolution_method	—
num_particles	195750

fit	/app/data/saxs_computation/zp/9zpy/9zpy.fit
pddf	/app/data/pr_computation/zp/9zpy/9zpy.pr.out
profile	/app/data/saxs_computation/zp/9zpy/9zpy.dat