Cryo-EM structure of human V1aR in apo state at a resolution of 2.8 angstrom

Method: ELECTRON MICROSCOPY D_max: 89.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xb1
deposition_date	2025-10-23
title	Cryo-EM structure of human V1aR in apo state at a resolution of 2.8 angstrom
keywords	GPCR, small molecule, antagonist, nanobody, SIGNALING PROTEIN, 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	27.90 Å
rg_electron	27.19 Å
i0	47979100.00
molecular_weight	59486.0 kDa
excluded_volume	76738 Å³
envelope_volume	91873 Å³
shell_volume	28095 Å³
envelope_diameter	94.3 Å
shell_rg	34.18 Å
envelope_rg	27.37 Å
shape_rg	27.19 Å
total_rg	27.96 Å
total_atoms	8416
n_residues	512
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	89.2 Å
rg_real	27.86 Å
rg_real_error	0.58 Å
i0_real	4.7980e+07
i0_real_error	6.2600e+05
rg_reciprocal	27.88 Å
i0_reciprocal	47980000.0000
total_estimate	0.7163
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	87.6 Å
skewness	0.208
kurtosis	-0.632
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	8087000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 0.978; Smooth: 0.963

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	504370

description	Vasopressin V1a receptor
formula_weight	43695.1 kDa
mutation	S341C, N344K
src_method	man
entity_count	2

Cryo-EM structure of human V1aR in apo state at a resolution of 2.8 angstrom

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

description	CHOLESTEROL
formula_weight	386.7 kDa
src_method	syn
entity_count	2

fit	/app/data/saxs_computation/xb/9xb1/9xb1.fit
pddf	/app/data/pr_computation/xb/9xb1/9xb1.pr.out
profile	/app/data/saxs_computation/xb/9xb1/9xb1.dat

type	polypeptide(L)
strand_id	A,B
atom_count	8416