SAXSdb — 9vor

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1. Structure Basics

entry_id	9vor
deposition_date	2025-07-02
title	Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20
keywords	GPCR, orphan receptor, nanobody, RGS proteins, signalling receptor, 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	54.89 Å
rg_electron	56.17 Å
i0	279975000.00
molecular_weight	153170.0 kDa
excluded_volume	197170 Å³
envelope_volume	314110 Å³
shell_volume	48467 Å³
envelope_diameter	179.1 Å
shell_rg	56.36 Å
envelope_rg	53.19 Å
shape_rg	56.16 Å
total_rg	56.25 Å
total_atoms	10796
n_residues	1322
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	167.6 Å
rg_real	55.29 Å
rg_real_error	1.49 Å
i0_real	2.8000e+08
i0_real_error	5.5660e+06
rg_reciprocal	54.52 Å
i0_reciprocal	279600000.0000
total_estimate	0.8154
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.2 Å
skewness	0.349
kurtosis	-0.801
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0000
highest_alpha	9612000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.801; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Metabotropic glycine receptor
formula_weight	88251.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10797

MGAMAYPLLLCLLLAQLGLGAVGASRDPQGRPDSPRERTPKGKPHAQQPGRASASDSSAPWSRSTDGTILAQKLAEEVPMDVASYLYTGDSHQLKRANCSGRYELAGLPGKWPALASAHPSLHRALDTLTHATNFLNVMLQSNKSREQNLQDDLDWYQALVWSLLEGEPSISRAAITFSTDSLSAPAPQVFLQATREESRILLQDLSSSAPHLANATLETEWFHGLRRKWRPHLHRRGPNQGPRGLGHSWRRKDGLGGDKSHFKWSPPYLECENGSYKPGWLVTLSSAIYGLQPNLVPEFRGVMKVDINLQKVDIDQCSSDGWFSGTHKCHLNNSECMPIKGLGFVLGAYECICKAGFYHPGVLPVNNFRRRGPDQHISGSTKDVSEEAYVCLPCREGCPFCADDSPCFVQEDKYLRLAIISFQALCMLLDFVSMLVVYHFRKAKSIRASGLILLETILFGSLLLYFPVVILYFEPSTFRCILLRWARLLGFATVYGTVTLKLHRVLKVFLSRTAQRIPYMTGGRVMRMLAVILLVVFWFLIGWTSSVCQNLEKQISLIGQGKTSDHLIFNMCLIDRWDYMTAVAEFLFLLWGVYLCYAVRTVPSAFHEPRYMAVAVHNELIISAIFHTIRFVLASRLQSDWMLMLYFAHTHLTVTVTIGLLLIPKFSHSSNNPRDDIATEAYEDELDMGRSGSYLNSSINSAWSEHSLDPEDIRDELKKLYAQLEIYKRKKMITNNPHLQKKRCSKKGLGRSIMRRITEIPETVSRQCSKEDKELEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Nb20
formula_weight	16722.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,E

MGSSHHHHHHHHLEVLFQGPAEVQLQESGGGLVQAGGSLRLSCAASGSIGNIYIMGWYRQTPGPQRELVATIRTVRWTKYEDYADSVKGRFTISDDDAKNTVYLQMNSLKPEDTAVYYCNYKDYNAPSDGYWGQGTQVTVSSEPKTPKPQ

Source

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

Entity 3 non-polymer

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	20

Entity 4 non-polymer

description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
formula_weight	744.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol
formula_weight	836.1 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	3.47 Å
resolution_method	—
num_particles	121523

fit	/app/data/saxs_computation/vo/9vor/9vor.fit
pddf	/app/data/pr_computation/vo/9vor/9vor.pr.out
profile	/app/data/saxs_computation/vo/9vor/9vor.dat

Cryo-EM Structure of Human GPR158 Bound to Nanobody Nb20

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 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)