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9qsx

Cryo-EM structure of aquaporin 3 at pH 8.0

Method: ELECTRON MICROSCOPY D_max: 86.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qsx
deposition_date	2025-04-07
title	Cryo-EM structure of aquaporin 3 at pH 8.0
keywords	membrane protein, glycerol channel, hydrogen peroxide transport, tetramer; 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	28.96 Å
rg_electron	28.24 Å
i0	333824000.00
molecular_weight	101580.0 kDa
excluded_volume	100600 Å³
envelope_volume	167160 Å³
shell_volume	46258 Å³
envelope_diameter	90.9 Å
shell_rg	37.86 Å
envelope_rg	28.33 Å
shape_rg	28.27 Å
total_rg	28.87 Å
total_atoms	7733
n_residues	1013
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	86.0 Å
rg_real	28.75 Å
rg_real_error	0.34 Å
i0_real	3.3380e+08
i0_real_error	4.3470e+06
rg_reciprocal	28.84 Å
i0_reciprocal	333800000.0000
total_estimate	0.9069
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.052
kurtosis	-0.561
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	64120000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.975

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Aquaporin-3
formula_weight	32396.5 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,C,B
atom_count	7741

MGRQKELVSRCGEMLHIRYRLLRQALAECLGTLILVMFGCGSVAQVVLSRGTHGGFLTINLAFGFAVTLGILIAGQVSGAHLNPAVTFAMCFLAREPWIKLPIYTLAQTLGAFLGAGIVFGLYYDAIWHFADNQLFVSGPNGTAGIFATYPSGHLDMINGFFDQFIGTASLIVCVLAIVDPYNNPVPRGLEAFTVGLVVLVIGTSMGFNSGYAVNPARDFGPRLFTALAGWGSAVFTTGQHWWWVPIVSPLLGSIAGVFVYQLMIGCHLEQPPPSNEEENVKLAHVKHKEQIHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Komagataella pastoris

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	fluorinated fos-choline-8
formula_weight	530.2 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.20 Å
resolution_method	—
num_particles	139031

fit	/app/data/saxs_computation/qs/9qsx/9qsx.fit
pddf	/app/data/pr_computation/qs/9qsx/9qsx.pr.out
profile	/app/data/saxs_computation/qs/9qsx/9qsx.dat

Cryo-EM structure of aquaporin 3 at pH 8.0

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