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9uyn

Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state

Method: ELECTRON MICROSCOPY D_max: 119.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uyn
deposition_date	2025-05-15
title	Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state
keywords	;G protein-coupled receptor 1, chemerin, beta-arrestin1, signaling 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	36.51 Å
rg_electron	36.45 Å
i0	159120000.00
molecular_weight	106240.0 kDa
excluded_volume	134900 Å³
envelope_volume	176870 Å³
shell_volume	41907 Å³
envelope_diameter	128.0 Å
shell_rg	40.85 Å
envelope_rg	36.36 Å
shape_rg	36.48 Å
total_rg	36.67 Å
total_atoms	7503
n_residues	961
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	36.63 Å
rg_real_error	1.01 Å
i0_real	1.5910e+08
i0_real_error	2.5000e+06
rg_reciprocal	36.56 Å
i0_reciprocal	159100000.0000
total_estimate	0.8804
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.5 Å
skewness	0.379
kurtosis	-0.416
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	25350000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.748

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Chemerin-like receptor 2,Vasopressin V2 receptor
formula_weight	48035.9 kDa
mutation	V143C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R
atom_count	7503

MKTIIALSYIFCLVFAGSWSHPQFEKGSGAGASAGSWSHPQFEKGSDYKDDDDKEFLEVLFQGPEDLEETLFEEFENYSYDLDYYSLESDLEEKVQLGVVHWVSLVLYCLAFVLGIPGNAIVIWFTGFKWKKTVTTLWFLNLAIADFIFLLFLPLYISYVAMNFHWPFGIWLCKANSFTAQLNMFASVFFLTVISLDHYIHLIHPCLSHRHRTLKNSLIVIIFIWLLASLIGGPALYFRDTVEFNNHTLCYNNFQKHDPDLTLIRHHVLTWVKFIIGYLFPLLTMSICYLCLIFKVKKRSILISSRHFWTILVVVVAFVVCWTPYHLFSIWELTIHHNSYSHHVMQAGIPLSTGLAFLNSCLNPILYVLISKKFQARFRSSVAEIARGRTPPSLGPQDESCTTASSSLAKDTSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Beta-arrestin-1
formula_weight	42107.1 kDa
mutation	C59A/C125S/C140I/C150V/R169E/C242V/Y249C/C251V/C269S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTAAFRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIPPNLPSSVTLQPGPEDTGKAIGVDYEVKAFVAENLEEKIHKRNSVRLVIEKVQYAPERPGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADIVLFNTAQCKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPPHREVPENETPVDTNL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Nanobody 32
formula_weight	13238.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

QVQLQESGGGLVQAGGSLRLSCVVSGFFFDTVTMAWYRRAPGKHRELVASATAGGTTTYADSVKDRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNTFVRSLSWGQGTQVTVSSHHHHHH

Source

organism	Escherichia phage EcSzw-2
ncbi_taxonomy_id	2419741
host_organism	Escherichia coli BL21

Entity 4 polymer

description	Single-chain fragment variable 30 (scFv30)
formula_weight	26157.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYKYVPVTFGQGTKVEIKGTTAASGSSGGSSSGAEVQLVESGGGLVQPGGSLRLSCAASGFNVYSSSIHWVRQAPGKGLEWVASISSYYGYTYYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARSRQFWYSGLDYWGQGTLVTVSSA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 non-polymer

description	PALMITOLEIC ACID
formula_weight	254.4 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	2.90 Å
resolution_method	—
num_particles	413367

fit	/app/data/saxs_computation/uy/9uyn/9uyn.fit
pddf	/app/data/pr_computation/uy/9uyn/9uyn.pr.out
profile	/app/data/saxs_computation/uy/9uyn/9uyn.dat

Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to beta-arrestin 1 in ligand-free state

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)