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- EMDB-64541: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan -

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Basic information

Entry
Database: EMDB / ID: EMD-64541
TitleCryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
Map data
Sample
  • Complex: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
    • Protein or peptide: Vasopressin V2 receptor,ARK1
  • Ligand: (R)-Tolvaptan
  • Ligand: water
KeywordsGPCR / V2R / vasopressin / tolvaptan / ARK1 / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / Resolution: 2.98 Å
AuthorsKojima A / Kawakami K / Kobayashi K / Matsui TE / Fukuda M / Kato HE
Funding support Japan, 6 items
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 TE / Uemoto K / Gu Y / Fukuda M / Kato HE
History
DepositionMay 11, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64541.png

Downloads & links

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Map

FileDownload / File: emd_64541.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.33514416 - 0.636411
Average (Standard dev.)-0.000531539 (±0.014557389)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64541_msk_1.map
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Additional map: #1

Fileemd_64541_additional_1.map
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Half map: #2

Fileemd_64541_half_map_1.map
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Half map: #1

Fileemd_64541_half_map_2.map
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Sample components

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

EntireName: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
Components
  • Complex: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
    • Protein or peptide: Vasopressin V2 receptor,ARK1
  • Ligand: (R)-Tolvaptan
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan

SupramoleculeName: Cryo-EM structure of Vasopressin receptor 2 (V2R)-ARK1 with tolvaptan
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vasopressin V2 receptor,ARK1

MacromoleculeName: Vasopressin V2 receptor,ARK1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.251109 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI FCLVFADYKD DDDAENLYFQ GMLMASTTSA VPGHPSLPSL PSNSSQERPL DTRDPLLARA ELALLSIVFV AVALSNGLV LAALARRGRR GHWAPIHVFI GHLCLADLAV ALFQVLPQLA WKATDRFRGP DALCRAVKYL QMVGMYASSY M ILAMTLDR ...String:
MKTIIALSYI FCLVFADYKD DDDAENLYFQ GMLMASTTSA VPGHPSLPSL PSNSSQERPL DTRDPLLARA ELALLSIVFV AVALSNGLV LAALARRGRR GHWAPIHVFI GHLCLADLAV ALFQVLPQLA WKATDRFRGP DALCRAVKYL QMVGMYASSY M ILAMTLDR HRAICRPMLA YRHGSGAHWN RPVLVAWAFS LLLSLPQLFI FAQRNVEGGS GVTDCWACFA EPWGRRTYVT WI ALMVFVA PTLGIAACQV LIFREIHASL ELRRLLREQG EKLLKLAEES EKKIKEAIEK GEDVVKVATE ETHKLIKAIW ESS FEVARL LGVPEEVLEK FRKELEKLLE ESKKRIEEAI KKGEDVLKVV EEEAKKLREH SEKFLETARS LGVDPRPLER LARI VRVVE ESLVRIVKAI KEGEDVEKVL LSESTLIKSS IILSSGLDPR EAYEELLATY EETRDSELVK EFVELVRELL RLRGE PEEL VRQLDKLIEA IDRMEKAVAE GEDTLPLFLE LAREILKALS DVARILAERE GLDVELIDEI VDTASRLLEE VIKKAK EGE DLDEEEEKVK KELEELKKRT EERARALGQD VELVRTIVDS LSTLLSEIVE GIKRVKEGED PLEVLARVVL TATLQIL EL VRTAERRRRE RVAKTVRMTL VIVVVYVLCW APFFLVQLWA AWDPEAPLEG APFVLLMLLA SLNSCTNPWI YASFSSSV S SELRSLLCCA RGRTPPSLGP QDESCTTASS SLAKDTSSLE VLFQ

UniProtKB: Vasopressin V2 receptor, Vasopressin V2 receptor

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Macromolecule #2: (R)-Tolvaptan

MacromoleculeName: (R)-Tolvaptan / type: ligand / ID: 2 / Number of copies: 1 / Formula: A1IT8
Molecular weightTheoretical: 448.941 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 201250
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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