SAXSdb — 9wsx

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1. Structure Basics

entry_id	9wsx
deposition_date	2025-09-15
title	Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex
keywords	G-protein-coupled receptors, mu-opioid receptor, single particle, Cryo-EM, 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	40.76 Å
rg_electron	41.26 Å
i0	172994000.00
molecular_weight	108400.0 kDa
excluded_volume	136430 Å³
envelope_volume	195000 Å³
shell_volume	41951 Å³
envelope_diameter	149.0 Å
shell_rg	42.72 Å
envelope_rg	41.60 Å
shape_rg	41.28 Å
total_rg	41.29 Å
total_atoms	7621
n_residues	1017
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	140.5 Å
rg_real	41.03 Å
rg_real_error	1.81 Å
i0_real	1.7300e+08
i0_real_error	3.2220e+06
rg_reciprocal	40.76 Å
i0_reciprocal	172900000.0000
total_estimate	0.8238
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.503
kurtosis	-0.188
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	12710000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.424

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Mu-type opioid receptor,Vasopressin V2 receptor
formula_weight	43316.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	7623

GPMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCICARGRTPPSLGPQDESCTTASSSLAKDTSSLEVLFQ

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Beta-arrestin-1
formula_weight	44135.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVEPVDGVVLVDPEYLKERRVYVTLTCAFRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIPPNLPCSVTLQPGPEDTGKACGVDYEVKAFCAENLEEKIHKRNSVRLVIEKVQYAPERPGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADICLFNTAQYKCPVAMEEADDTVAPSSTFCKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPPHREVPEHETPVDTNLIELDTNDDDAAAEDFAR

Source

organism	Bos taurus
common_name	domestic cattle
ncbi_taxonomy_id	9913
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Fab30 heavy chain
formula_weight	25333.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MEISEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTENLYFQ

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 4 polymer

description	Fab30 light chain
formula_weight	23566.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MSDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	synthetic construct
ncbi_taxonomy_id	32630
host_organism	Escherichia coli

Entity 5 polymer

description	endomorphin-1
formula_weight	609.7 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

YPWFX

Entity 6 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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	206690

fit	/app/data/saxs_computation/ws/9wsx/9wsx.fit
pddf	/app/data/pr_computation/ws/9wsx/9wsx.pr.out
profile	/app/data/saxs_computation/ws/9wsx/9wsx.dat

Cryo-EM structure of endomorphin-1-muOR-arrestin2-Fab30 complex

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)