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9w3f

Cryo-EM structure of the human beta2-adrenergic receptor in complex with a novel antagonist

Method: ELECTRON MICROSCOPY D_max: 96.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w3f
deposition_date	2025-07-29
title	Cryo-EM structure of the human beta2-adrenergic receptor in complex with a novel antagonist
keywords	Antagonist, membrane protein, GPCR; 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	26.90 Å
rg_electron	26.26 Å
i0	26489500.00
molecular_weight	42431.0 kDa
excluded_volume	54265 Å³
envelope_volume	64816 Å³
shell_volume	22599 Å³
envelope_diameter	98.6 Å
shell_rg	30.87 Å
envelope_rg	26.74 Å
shape_rg	26.27 Å
total_rg	26.80 Å
total_atoms	2992
n_residues	393
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	96.1 Å
rg_real	27.27 Å
rg_real_error	1.04 Å
i0_real	2.6490e+07
i0_real_error	4.4800e+05
rg_reciprocal	27.16 Å
i0_reciprocal	26490000.0000
total_estimate	0.7830
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.8 Å
skewness	0.618
kurtosis	-0.212
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	6171000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.616; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.394; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Beta-2 adrenergic receptor,Endolysin
formula_weight	58532.8 kDa
ec_number	3.2.1.17
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2993

MKTIIALSYIFCLVFADYKDDDDAMGQPGNGSAFLLAPNRSHAPDHDVTQQRDEVWVVGMGIVMSLIVLAIVFGNVLVITAIAKFERLQTVTNYFITSLACADLVMGLAVVPFGAAHILMKMWTFGNFWCEFWTSIDVLCVTASIETLCVIAVDRYFAITSPFKYQSLLTKNKARVIILMVWIVSGLTSFLPIQMHWYRATHQEAINCYAEETCCDFFTNQAYAIASSIVSFYVPLVIMVFVYSRVFQEAKRQLNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKFCLKEHKALKTLGIIMGTFTLCWLPFFIVNIVHVIQDNLIRKEVYILLNWIGYVNSGFNPLIYCRSPDFRIAFQELLCLRRSSLKAYGNGYSSNGNTGEQSG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera

Entity 2 polymer

description	Beta2 adrenogic receptor inactive-state stabling nanobody Nb60
formula_weight	13531.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLQESGGGLVQAGGSLRLSCAASGSIFSLNDMGWYRQAPGKLRELVAAITSGGSTKYADSVKGRFTISRDNAKNTVYLQMNSLKAEDTAVYYCNAKVAGTFSIYDYWGQGTQVTVSSHHHHHH

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 3 non-polymer

description	BERBERINE
formula_weight	336.4 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
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	3.040 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.04 Å
resolution_method	—
num_particles	347166

fit	/app/data/saxs_computation/w3/9w3f/9w3f.fit
pddf	/app/data/pr_computation/w3/9w3f/9w3f.pr.out
profile	/app/data/saxs_computation/w3/9w3f/9w3f.dat

Cryo-EM structure of the human beta2-adrenergic receptor in complex with a novel antagonist

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)