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9ucp

cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4

Method: ELECTRON MICROSCOPY D_max: 108.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ucp
deposition_date	2025-04-05
title	cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4
keywords	GPCR, active-state, nanobody, de novo protein, MEMBRANE PROTEIN/IMMUNE SYSTEM, MEMBRANE PROTEIN-IMMUNE SYSTEM complex; MEMBRANE PROTEIN/IMMUNE SYSTEM
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	29.88 Å
rg_electron	29.69 Å
i0	41024200.00
molecular_weight	49919.0 kDa
excluded_volume	62277 Å³
envelope_volume	81605 Å³
shell_volume	25352 Å³
envelope_diameter	112.2 Å
shell_rg	33.07 Å
envelope_rg	30.52 Å
shape_rg	29.69 Å
total_rg	30.02 Å
total_atoms	3529
n_residues	511
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	108.3 Å
rg_real	30.35 Å
rg_real_error	1.14 Å
i0_real	4.1020e+07
i0_real_error	6.4210e+05
rg_reciprocal	30.15 Å
i0_reciprocal	41020000.0000
total_estimate	0.7452
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	24.5 Å
skewness	0.681
kurtosis	-0.137
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	14500000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.483; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.387; Smooth: 0.850

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	M1 muscarinic acetylcholine receptor, de novo design protein
formula_weight	49317.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3529

DYKDDDDAAAQTSAPPAVSPQITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLALDYVASNASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLYWRIYRETKRAGERLAKLLEKFEALPLEDIVAALKALLATNRPEIQLAVKTIVENFPEIKKEAEKLTPEQKAKLAALEAQLADLPEELRKVLLSMYLTGLLYGGSEENRKRAIEKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNSTINPMCYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQCHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Guanine nucleotide-binding protein subunit alpha-11
formula_weight	3152.7 kDa
ec_number	3.6.5.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

TPENIRFVFAAVKDTILQLNLKEYNLV

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Nanobody Nb1B4
formula_weight	13766.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

QVQLQESGGGLVQAGGSLRLSCAASGSIFYGYYMGWYRQAPGKEREFVATINYGASTNYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVRRVYVYVQRYYHYYWGQGTQVTVSS

Source

organism	Vicugna pacos
ncbi_taxonomy_id	30538
host_organism	Homo sapiens

Entity 4 non-polymer

description	4-(4,5-dihydro-1,2-oxazol-3-yloxy)-N,N,N-trimethylbut-2-yn-1-aminium
formula_weight	197.3 kDa
src_method	syn
entity_count	1

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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	2.88 Å
resolution_method	—
num_particles	191008

fit	/app/data/saxs_computation/uc/9ucp/9ucp.fit
pddf	/app/data/pr_computation/uc/9ucp/9ucp.pr.out
profile	/app/data/saxs_computation/uc/9ucp/9ucp.dat

cryo-EM structure of M1 muscarinic acetylcholine receptor-alpha5 helix of G11 protein complex bound to iperoxo and nanobody Nb1B4

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)