SAXSdb — 9wsw

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1. Structure Basics

entry_id	9wsw
deposition_date	2025-09-15
title	Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 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	34.88 Å
rg_electron	35.06 Å
i0	155400000.00
molecular_weight	101680.0 kDa
excluded_volume	127980 Å³
envelope_volume	166180 Å³
shell_volume	40802 Å³
envelope_diameter	126.0 Å
shell_rg	39.91 Å
envelope_rg	35.21 Å
shape_rg	35.06 Å
total_rg	35.40 Å
total_atoms	7132
n_residues	901
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	119.0 Å
rg_real	35.02 Å
rg_real_error	1.01 Å
i0_real	1.5540e+08
i0_real_error	2.7870e+06
rg_reciprocal	34.93 Å
i0_reciprocal	155400000.0000
total_estimate	0.8645
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.4 Å
skewness	0.448
kurtosis	-0.273
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	30450000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.930; Smooth: 0.770

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Engineered guanine nucleotide-binding protein G(z) subunit alpha
formula_weight	40699.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7134

MGCTLSAEDKAAVERSKMIDRNLREDGEKQRREIKLLLLGTSNSGKNTIVKQMKIIHSGGFNLEACKEYKPLIIYNAIDSLTRIIRALAALRIDFHNPDRAYDAVQLFALTGPAESKGEITPELLGVMRRLWADPGAQACFSRSSEYHLEDNAAYYLNDLERIAAADYIPTVEDILRSRDMTTGIVENKFTFKELTFKMVDVGAQRSERKKWIHCFEGVTAIIFCVELSGYDLKLYEDNQTSRMAASLKLFDSICNNKWFIDTSLILFLNKKDLLAEKIRRIPLTICFPEYKGQNTYEEAAVYIQRQFEDLNRNKETKEIYSHFTCSTDTSNIQFVFDAVTDVIIQNNLKYIGLC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
formula_weight	40039.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSGVSGWRLFKKIS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
formula_weight	7861.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Mu-type opioid receptor,Vasopressin V2 receptor
formula_weight	42836.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

GPMGPGNISDCSDPLAPASCSPAPGSWLNLSHVDGNQSDPCGPNRTGLGGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCICARGRTPPSLGPQDESCTTASSSLAKDTSSLEVLFQ

Source

organism	Homo sapiens
common_name	Human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

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	149926

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

Cryo-EM structure of endomorphin-1-muOR-Gz-scFv16 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)