9UVY | pdb_00009uvy

Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan

PDB DOI: https://doi.org/10.2210/pdb9UVY/pdb
EM Map EMD-64541: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-05-11 Released: 2026-05-06
Deposition Author(s): Kojima, A., Kawakami, K., Kobayashi, K., Matsui, T.E., Fukuda, M., Kato, H.E.
Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9UVY

This is version 1.0 of the entry. See complete history.

Literature

A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design

Kojima, A., Kawakami, K., Kobayashi, N., Kobayashi, K., Matsui, T.E., Uemoto, K., Gu, Y., Fukuda, M., Kato, H.E.

(2026) bioRxiv

DOI: https://doi.org/10.64898/2026.04.02.716066

Macromolecule Content

Total Structure Weight: 86.7 kDa
Atom Count: 5,247
Modeled Residue Count: 653
Deposited Residue Count: 765
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vasopressin V2 receptor,ARK1	A	765	Homo sapiens, synthetic construct	Mutation(s): 0 Gene Names: AVPR2, ADHR, DIR, DIR3, V2R
UniProt & NIH Common Fund Data Resources
Find proteins for P30518 (Homo sapiens) Explore P30518 Go to UniProtKB: P30518
PHAROS: P30518 GTEx: ENSG00000126895
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30518
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1IT8 (Subject of Investigation/LOI) Query on A1IT8 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(R)-Tolvaptan C₂₆ H₂₅ Cl N₂ O₃ GYHCTFXIZSNGJT-XMMPIXPASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.98 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJAX222F
Japan Science and Technology	Japan	JPMJPR24OF
Japan Society for the Promotion of Science (JSPS)	Japan	25K09525
Japan Society for the Promotion of Science (JSPS)	Japan	24H02262
Japan Society for the Promotion of Science (JSPS)	Japan	25H01338
Japan Society for the Promotion of Science (JSPS)	Japan	JP24KJ0981

Revision History (Full details and data files)

Version 1.0: 2026-05-06
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.