SAXSdb — 9wst

▼

1. Structure Basics

entry_id	9wst
deposition_date	2025-09-15
title	Cryo-EM structure of DAMGO-muOR-Gz-scFv16 complex
keywords	G-protein-coupled receptors, mu-opioid receptor, single particle, Cryo-EM, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	34.76 Å
rg_electron	34.90 Å
i0	153954000.00
molecular_weight	101110.0 kDa
excluded_volume	127260 Å³
envelope_volume	164730 Å³
shell_volume	40748 Å³
envelope_diameter	127.4 Å
shell_rg	39.67 Å
envelope_rg	34.95 Å
shape_rg	34.89 Å
total_rg	35.27 Å
total_atoms	7089
n_residues	897
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

▼

3. P(r) Analysis (GNOM)

dmax	119.2 Å
rg_real	34.90 Å
rg_real_error	1.52 Å
i0_real	1.5400e+08
i0_real_error	3.1830e+06
rg_reciprocal	34.81 Å
i0_reciprocal	153900000.0000
total_estimate	0.8655
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	114.0 Å
skewness	0.451
kurtosis	-0.262
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	32690000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.844

▶

4. Crystallography & Experiment

▶

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	7090

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,LgBiT
formula_weight	64018.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

DYKDDDDKGPGNISDCSDPLAPASCSPAPSPGSWLNLSHVDGNQSDPCGPNRTGLGGSHSLCPQTGSPSMVTAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGNILCKIVISIDYYNMFTSIFTLCTMSVDRYIAVCHPVKALDFRTPRNAKIVNVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALITIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSTIEQQNSARIRQNTREHPSTANTVDRTNHQLENLEAETAPLPGGSSGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINSGGSLEVLFQ

Source

organism	Oplophorus gracilirostris
ncbi_taxonomy_id	727944
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	DAMGO
formula_weight	513.6 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	P

YAGFX

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

▶

6. Citations (1)

▶

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	136606

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

Cryo-EM structure of DAMGO-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)