Structure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)

Method: ELECTRON MICROSCOPY D_max: 114.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qju
deposition_date	2025-03-19
title	Structure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)
keywords	lipid Transport, membrane contact sites, scramblase, TMEM16 protein, 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	36.88 Å
rg_electron	35.97 Å
i0	160257000.00
molecular_weight	115020.0 kDa
excluded_volume	149180 Å³
envelope_volume	196070 Å³
shell_volume	46194 Å³
envelope_diameter	124.5 Å
shell_rg	41.83 Å
envelope_rg	35.37 Å
shape_rg	35.94 Å
total_rg	36.54 Å
total_atoms	8152
n_residues	990
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	114.9 Å
rg_real	36.80 Å
rg_real_error	0.74 Å
i0_real	1.6030e+08
i0_real_error	2.5630e+06
rg_reciprocal	36.85 Å
i0_reciprocal	160300000.0000
total_estimate	0.9046
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	42.8 Å
skewness	0.187
kurtosis	-0.603
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	16200000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.842

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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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	3.340 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.34 Å
resolution_method	—
num_particles	189991

description	Increased sodium tolerance protein 2
formula_weight	87777.4 kDa
src_method	man
entity_count	2

Structure of the transmembrane domain of Ist2 in lipid nanodiscs (narrow state)

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

Refinement

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Saccharomyces cerevisiae

fit	/app/data/saxs_computation/qj/9qju/9qju.fit
pddf	/app/data/pr_computation/qj/9qju/9qju.pr.out
profile	/app/data/saxs_computation/qj/9qju/9qju.dat

type	polypeptide(L)
strand_id	B,A
atom_count	8152