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9u81

Cryo-EM structure of tolvaptan-bound human vasopressin V2 receptor complex with Fab

Method: ELECTRON MICROSCOPY D_max: 143.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u81
deposition_date	2025-03-25
last_revision	2025-12-10
title	Cryo-EM structure of tolvaptan-bound human vasopressin V2 receptor complex with Fab
keywords	GPCR, vasopressin V2 receptor, antagonist, tolvaptan, 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	41.76 Å
rg_electron	42.57 Å
i0	114835000.00
molecular_weight	88929.0 kDa
excluded_volume	111960 Å³
envelope_volume	161270 Å³
shell_volume	33998 Å³
envelope_diameter	145.3 Å
shell_rg	43.27 Å
envelope_rg	42.19 Å
shape_rg	42.67 Å
total_rg	42.27 Å
total_atoms	12441
n_residues	816
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	143.2 Å
rg_real	42.19 Å
rg_real_error	1.69 Å
i0_real	1.1480e+08
i0_real_error	2.0680e+06
rg_reciprocal	41.77 Å
i0_reciprocal	114800000.0000
total_estimate	0.7737
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	30.1 Å
skewness	0.459
kurtosis	-0.674
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	9164000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.634; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.535; Smooth: 0.619

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	anti-BRIL Fab heavy chain
formula_weight	24321.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	12441

ELSEVQLVESGGGLVQPGGSLRLSCAASGFNVVDFSLHWVRQAPGKGLEWVAYISSSSGSTSYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWGYWPGEPWWKAFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 2 polymer

description	anti-BRIL Fab light chain
formula_weight	23586.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SDIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQYLYYSLVTFGQGTKVEIKRTVAAPSVFIFPPSDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 3 polymer

description	Vasopressin V2 receptor,Soluble cytochrome b562
formula_weight	50571.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MLMASTTSAVPGHPSLPSLPSNSSQERPLDTRDPLLARAELALLSIVFVAVALSNGLVLAALARRGRRGHWAPIHVFIGHLCLADLAVALFQVLPQLAWKATDRFRGPDALCRAVKYLQMVGMYASSYMILAMTLDRHRAICRPMLAYRHGSGAHWNRPVLVAWAFSLLLSLPQLFIFAQRNVEGGSGVTDCWACFAEPWGRRTYVTWIALMVFVAPTLGIAACQVLIFREIHAARRQLADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLERARSTLAAVAKTVRMTLVIVVVYVLCWAPFFLVQLWAAWDPEAPLEGAPFVLLMLLASLNSCTNPWIYASFSSSVSSELRSLLCCARGRTPPSLGPQDESCTTASSSLAKDTSS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Trichoplusia ni

Entity 4 non-polymer

description	Tolvaptan
formula_weight	448.9 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	3.080 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.08 Å
resolution_method	—
num_particles	326036

fit	/app/data/saxs_computation/u8/9u81/9u81.fit
pddf	/app/data/pr_computation/u8/9u81/9u81.pr.out
profile	/app/data/saxs_computation/u8/9u81/9u81.dat

Cryo-EM structure of tolvaptan-bound human vasopressin V2 receptor complex with Fab

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 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)