SAXSdb — 9pu5

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1. Structure Basics

entry_id	9pu5
deposition_date	2025-07-30
title	Cryo-EM structure of human MOR-Gi1 complex protein bound with DAMGO and BMS986187
keywords	analgesics, GPCR, allosteric modulation, 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	53.65 Å
rg_electron	53.36 Å
i0	1174070000.00
molecular_weight	191140.0 kDa
excluded_volume	186150 Å³
envelope_volume	380670 Å³
shell_volume	64265 Å³
envelope_diameter	192.7 Å
shell_rg	49.92 Å
envelope_rg	52.77 Å
shape_rg	53.26 Å
total_rg	53.45 Å
total_atoms	14440
n_residues	1811
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	190.9 Å
rg_real	54.15 Å
rg_real_error	2.40 Å
i0_real	1.1740e+09
i0_real_error	2.1930e+07
rg_reciprocal	53.21 Å
i0_reciprocal	1172000000.0000
total_estimate	0.7971
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.1 Å
skewness	0.525
kurtosis	-0.494
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	33920000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.639; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.778; Smooth: 0.663

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Guanine nucleotide-binding protein G(i) subunit alpha-1
formula_weight	40414.0 kDa
ec_number	3.6.5.-
mutation	S47N, G203A, E245A, A326S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	14466

MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Source

organism	Homo sapiens
common_name	human
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	37561.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,C

MSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

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	8506.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,E

MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAILGSAGSAGSA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Mu-type opioid receptor
formula_weight	43577.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,F

MDSSAAPTNASNCTDALAYSSCSPAPSPGSWVNLSHLDGNLSDPCGPNRTDLGGRDSLCPPTGSPSMITAITIMALYSIVCVVGLFGNFLVMYVIVRYTKMKTATNIYIFNLALADALATSTLPFQSVNYLMGTWPFGTILCKIVISIDYYNMFTSIWTLCTMSVDRYIAVCHPVKALDFRTPRNAKIINVCNWILSSAIGLPVMFMATTKYRQGSIDCTLTFSHPTWYWENLLKICVFIFAFIMPVLIITVCYGLMILRLKSVRMLSGSKEKDRNLRRITRMVLVVVAVFIVCWTPIHIYVIIKALVTIPETTFQTVSWHFCIALGYTNSCLNPVLYAFLDENFKRCFREFCIPTSSNIEQQNSTRIRQNTRDHPSTANTVDRTNHQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	DAMGO
formula_weight	513.6 kDa
src_method	syn
entity_count	2

Polymer

type	polypeptide(L)
strand_id	S,H

YAGFX

Entity 6 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	8

Entity 7 non-polymer

description	3,3,6,6-tetramethyl-9-[4-[(2-methylphenyl)methoxy]phenyl]-4,5,7,9-tetrahydro-2~{H}-xanthene-1,8-dione
formula_weight	470.6 kDa
src_method	syn
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	3.50 Å
resolution_method	—
num_particles	101558

fit	/app/data/saxs_computation/pu/9pu5/9pu5.fit
pddf	/app/data/pr_computation/pu/9pu5/9pu5.pr.out
profile	/app/data/saxs_computation/pu/9pu5/9pu5.dat

Cryo-EM structure of human MOR-Gi1 complex protein bound with DAMGO and BMS986187

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 (7)

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 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)