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- PDB-9uvy: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan -

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Basic information

Entry
Database: PDB / ID: 9uvy
TitleCryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
ComponentsVasopressin V2 receptor,ARK1
KeywordsMEMBRANE PROTEIN / GPCR / V2R / vasopressin / tolvaptan / ARK1
Function / homology
Function and homology information


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / renal water absorption / hemostasis / telencephalon development / positive regulation of systemic arterial blood pressure / positive regulation of intracellular signal transduction ...renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / renal water absorption / hemostasis / telencephalon development / positive regulation of systemic arterial blood pressure / positive regulation of intracellular signal transduction / positive regulation of vasoconstriction / endocytic vesicle / activation of adenylate cyclase activity / cellular response to hormone stimulus / response to cytokine / clathrin-coated endocytic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / endosome / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Vasopressin V2 receptor / Vasopressin receptor / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
: / Vasopressin V2 receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.98 Å
AuthorsKojima, A. / Kawakami, K. / Kobayashi, K. / Matsui, T.E. / Fukuda, M. / Kato, H.E.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJAX222F Japan
Japan Science and TechnologyJPMJPR24OF Japan
Japan Society for the Promotion of Science (JSPS)25K09525 Japan
Japan Society for the Promotion of Science (JSPS)24H02262 Japan
Japan Society for the Promotion of Science (JSPS)25H01338 Japan
Japan Society for the Promotion of Science (JSPS)JP24KJ0981 Japan
CitationJournal: Biorxiv / Year: 2026
Title: A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design
Authors: Kojima, A. / Kawakami, K. / Kobayashi, N. / Kobayashi, K. / Matsui, T.E. / Uemoto, K. / Gu, Y. / Fukuda, M. / Kato, H.E.
History
DepositionMay 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vasopressin V2 receptor,ARK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,7002
Polymers86,2511
Non-polymers4491
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Vasopressin V2 receptor,ARK1 / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor


Mass: 86251.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: AVPR2, ADHR, DIR, DIR3, V2R / Production host: Homo sapiens (human) / References: UniProt: P30518
#2: Chemical ChemComp-A1IT8 / (R)-Tolvaptan


Mass: 448.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25ClN2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21synthetic construct (others)32630
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 45.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201250 / Symmetry type: POINT
RefinementResolution: 2.98→2.98 Å / Cor.coef. Fo:Fc: 0.827 / WRfactor Rwork: 0.395 / SU B: 14.987 / SU ML: 0.235 / Average fsc free: 0 / Average fsc overall: 0.6774 / Average fsc work: 0.6774 / ESU R: 0.391
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3948 69226 -
all0.395 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 108.425 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0125324
ELECTRON MICROSCOPYr_bond_other_d00.0165386
ELECTRON MICROSCOPYr_ext_dist_refined_b0.0010.186398
ELECTRON MICROSCOPYr_angle_refined_deg1.6571.8727193
ELECTRON MICROSCOPYr_angle_other_deg0.6621.76512383
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.1655650
ELECTRON MICROSCOPYr_dihedral_angle_2_deg14.3992.860
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.163101027
ELECTRON MICROSCOPYr_dihedral_angle_6_deg11.24210227
ELECTRON MICROSCOPYr_chiral_restr0.090.2850
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.026178
ELECTRON MICROSCOPYr_gen_planes_other0.0030.021158
ELECTRON MICROSCOPYr_nbd_refined0.2210.21244
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1480.24864
ELECTRON MICROSCOPYr_nbtor_refined0.1650.22627
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0640.23113
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1780.287
ELECTRON MICROSCOPYr_mcbond_it9.8239.7012609
ELECTRON MICROSCOPYr_mcbond_other9.829.7012609
ELECTRON MICROSCOPYr_mcangle_it16.11617.4633256
ELECTRON MICROSCOPYr_mcangle_other16.11417.4663257
ELECTRON MICROSCOPYr_scbond_it13.1911.9112715
ELECTRON MICROSCOPYr_scbond_other13.18811.9092716
ELECTRON MICROSCOPYr_scangle_it22.82420.9073937
ELECTRON MICROSCOPYr_scangle_other22.82120.9033938
ELECTRON MICROSCOPYr_lrange_it39.124211.57487138
ELECTRON MICROSCOPYr_lrange_other39.123211.57387139
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3-3.0781.30352051.30352050.1591.303
3.078-3.1620.84549090.84549090.2030.845
3.162-3.2540.8148360.8148360.2660.81
3.254-3.3540.78847620.78847620.380.788
3.354-3.4640.6845970.6845970.5130.68
3.464-3.5850.52244420.52244420.6650.522
3.585-3.7210.37941960.37941960.7890.379
3.721-3.8720.29841090.29841090.8790.298
3.872-4.0440.29239020.29239020.9180.292
4.044-4.2420.30238040.30238040.9410.302
4.242-4.4710.31135540.31135540.9530.311
4.471-4.7420.30733780.30733780.9610.307
4.742-5.0690.28531890.28531890.9610.285
5.069-5.4740.26329240.26329240.9470.263
5.474-5.9960.27327780.27327780.9010.273
5.996-6.7020.33424110.33424110.8520.334
6.702-7.7350.37221970.37221970.8350.372
7.735-9.4660.33618500.33618500.8950.336
9.466-13.3550.28913970.28913970.9370.289
13.355-136.120.8897860.8897860.9590.889

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