SAXSdb — 9uyj

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1. Structure Basics

entry_id	9uyj
deposition_date	2025-05-15
title	Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 1 (Conformation 3)
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	37.94 Å
rg_electron	37.81 Å
i0	157893000.00
molecular_weight	103950.0 kDa
excluded_volume	131140 Å³
envelope_volume	179260 Å³
shell_volume	41411 Å³
envelope_diameter	132.1 Å
shell_rg	41.52 Å
envelope_rg	37.54 Å
shape_rg	37.85 Å
total_rg	37.93 Å
total_atoms	7346
n_residues	953
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	130.1 Å
rg_real	38.10 Å
rg_real_error	1.64 Å
i0_real	1.5790e+08
i0_real_error	3.0320e+06
rg_reciprocal	38.01 Å
i0_reciprocal	157900000.0000
total_estimate	0.8747
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.4 Å
skewness	0.371
kurtosis	-0.454
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	22960000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; Smooth: 0.853

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-arrestin-1
formula_weight	42167.1 kDa
mutation	C59A, C125S, C140I, C150V, R169E, C242V, C251V and C269S
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	7346

MGDKGTRVFKKASPNGKLTVYLGKRDFVDHIDLVDPVDGVVLVDPEYLKERRVYVTLTAAFRYGREDLDVLGLTFRKDLFVANVQSFPPAPEDKKPLTRLQERLIKKLGEHAYPFTFEIPPNLPSSVTLQPGPEDTGKAIGVDYEVKAFVAENLEEKIHKRNSVRLVIEKVQYAPERPGPQPTAETTRQFLMSDKPLHLEASLDKEIYYHGEPISVNVHVTNNTNKTVKKIKISVRQYADIVLFNTAQYKVPVAMEEADDTVAPSSTFSKVYTLTPFLANNREKRGLALDGKLKHEDTNLASSTLLREGANREILGIIVSYKVKVKLVVSRGGLLGDLASSDVAVELPFTLMHPKPKEEPPHREVPENETPVDTNL

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 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 3 polymer

description	Chemerin-like receptor 2,Vasopressin V2 receptor
formula_weight	45991.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

WSHPQFEKGSGAGASAGSWSHPQFEKGSDYKDDDDKEFLEVLFQGPEDLEETLFEEFENYSYDLDYYSLESDLEEKVQLGVVHWVSLVLYCLAFVLGIPGNAIVIWFTGFKWKKTVTTLWFLNLAIADFIFLLFLPLYISYVAMNFHWPFGIWLCKANSFTAQLNMFASVFFLTVISLDHYIHLIHPVLSHRHRTLKNSLIVIIFIWLLASLIGGPALYFRDTVEFNNHTLCYNNFQKHDPDLTLIRHHVLTWVKFIIGYLFPLLTMSICYLCLIFKVKKRSILISSRHFWTILVVVVAFVVCWTPYHLFSIWELTIHHNSYSHHVMQAGIPLSTGLAFLNSCLNPILYVLISKKFQARFRSSVAEIARGRTPPSLGPQDESCTTASSSLAKDTSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Retinoic acid receptor responder protein 2
formula_weight	17720.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MKTIIALSYIFCLVFAELTEAQRRGLQVALEEFHKHPPVQWAFQETSVESAVDTPFPAGIFVRLEFKLQQTSCRKRDWKKPECKVRPNGRKRKCLACIKLGSEDKVLGRLVHCPIETQVLREAEEHQETQCLRVQRAGEDPHSFYFPGQFAFS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 5 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

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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	3.300 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.30 Å
resolution_method	—
num_particles	132110

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

Cryo-EM structure of the G protein-coupled receptor 1 (GPR1) bound to chemerin and beta-arrestin 1 (Conformation 3)

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)