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9zd2

C1 local refinement of aquaporin 1 bound to endogenous human stomatin

Method: ELECTRON MICROSCOPY D_max: 130.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zd2
deposition_date	2025-11-24
title	C1 local refinement of aquaporin 1 bound to endogenous human stomatin
keywords	Oligomer, C8 symmetry, scaffold, 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	42.68 Å
rg_electron	41.85 Å
i0	567881000.00
molecular_weight	209080.0 kDa
excluded_volume	267560 Å³
envelope_volume	379880 Å³
shell_volume	73723 Å³
envelope_diameter	128.6 Å
shell_rg	49.69 Å
envelope_rg	40.16 Å
shape_rg	41.86 Å
total_rg	42.22 Å
total_atoms	14755
n_residues	1958
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	130.3 Å
rg_real	42.46 Å
rg_real_error	0.87 Å
i0_real	5.6790e+08
i0_real_error	9.5610e+06
rg_reciprocal	42.68 Å
i0_reciprocal	568000000.0000
total_estimate	0.8343
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	52.8 Å
skewness	0.006
kurtosis	-0.769
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	60200000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Aquaporin-1
formula_weight	25996.1 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,B,C,A
atom_count	14799

SEFKKKLFWRAVVAEFLATTLFVFISIGSALGFKYPVGNNQTAVQDNVKVSLAFGLSIATLAQSVGHISGAHLNPAVTLGLLLSCQISIFRALMYIIAQCVGAIVATAILSGITSSLTGNSLGRNDLADGVNSGQGLGIEIIGTLQLVLCVLATTDRRRRDLGGSAPLAIGLSVALGHLLAIDYTGCGINPARSFGSAVITHNFSNHWIFWVGPFIGGALAVLIYDFILAPRSSDLTDRVKVWTSGQ

Entity 2 polymer

description	Stomatin
formula_weight	21128.7 kDa
src_method	nat
entity_count	5

Polymer

type	polypeptide(L)
strand_id	F,G,E,I,H

XXXXXXXXXXXXXXXXXXKGLGPCGWILVAFSFLFTVITFPISIWMCIKIIKEYERAIIFRLGRILQGGAKGPGLFFILPCTDSFIKVDMRTISFDIPPQEILTKDSVTISVDGVVYYRVQNATLAVANITNADSATRLLAQTTLRNVLGTKNLSQILSDREEIAHNMQSTLDDATDAWGIKVERVEIKDVKLP

Entity 3 non-polymer

description	PALMITIC ACID
formula_weight	256.4 kDa
src_method	nat
entity_count	4

Entity 4 non-polymer

description	CHOLESTEROL
formula_weight	386.7 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	3.10 Å
resolution_method	—
num_particles	135000

fit	/app/data/saxs_computation/zd/9zd2/9zd2.fit
pddf	/app/data/pr_computation/zd/9zd2/9zd2.pr.out
profile	/app/data/saxs_computation/zd/9zd2/9zd2.dat

C1 local refinement of aquaporin 1 bound to endogenous human stomatin

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

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)