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- EMDB-64538: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL ... -

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Basic information

Entry
Database: EMDB / ID: EMD-64538
TitleCryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
Map data
Sample
  • Complex: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
    • Complex: Vasopressin receptor 2 (V2R)-BRIL
      • Protein or peptide: Vasopressin V2 receptor,Soluble cytochrome b562
    • Complex: anti BRIL SRP2070 Fab antibody
      • Protein or peptide: Light chain of anti-BRIL SRP2070 fab antibody
      • Protein or peptide: Heavy chain of anti-BRIL SRP2070 fab antibody
  • Ligand: (R)-Tolvaptan
KeywordsGPCR / V2R / vasopressin / tolvaptan / 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 / electron transport chain / 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 / periplasmic space / electron transfer activity / endosome / iron ion binding / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / heme binding / 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / Vasopressin V2 receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / Resolution: 3.02 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)24KJ0981 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_64538.png

Downloads & links

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Map

FileDownload / File: emd_64538.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 210 pix.
= 174.3 Å		0.83 Å/pix.
x 210 pix.
= 174.3 Å		0.83 Å/pix.
x 210 pix.
= 174.3 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.2964479 - 0.57030404
Average (Standard dev.)-0.00003353612 (±0.022544215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 174.3 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64538_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_64538_additional_1.map
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Half map: #2

Fileemd_64538_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_64538_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL ...

EntireName: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
Components
  • Complex: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
    • Complex: Vasopressin receptor 2 (V2R)-BRIL
      • Protein or peptide: Vasopressin V2 receptor,Soluble cytochrome b562
    • Complex: anti BRIL SRP2070 Fab antibody
      • Protein or peptide: Light chain of anti-BRIL SRP2070 fab antibody
      • Protein or peptide: Heavy chain of anti-BRIL SRP2070 fab antibody
  • Ligand: (R)-Tolvaptan

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Supramolecule #1: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL ...

SupramoleculeName: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Vasopressin receptor 2 (V2R)-BRIL

SupramoleculeName: Vasopressin receptor 2 (V2R)-BRIL / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: anti BRIL SRP2070 Fab antibody

SupramoleculeName: anti BRIL SRP2070 Fab antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Vasopressin V2 receptor,Soluble cytochrome b562

MacromoleculeName: Vasopressin V2 receptor,Soluble cytochrome b562 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 53.594973 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 ADLEDNWETL NDNLKVIEKA DNAAQVKDAL TKMRAAALDA QKATPPKLED KSP DSPEMK DFRHGFDILV GQIDDALKLA NEGKVKEAQA AAEQLKTTRN AYIQKYLAVA KTVRMTLVIV VVYVLCWAPF FLVQ LWAAW DPEAPLEGAP FVLLMLLASL NSCTNPWIYA SFSSSVSSEL RSLLCCARGR TPPSLGPQDE SCTTASSSLA KDTSS LEVL FQ

UniProtKB: Vasopressin V2 receptor, Soluble cytochrome b562, Vasopressin V2 receptor

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Macromolecule #2: Light chain of anti-BRIL SRP2070 fab antibody

MacromoleculeName: Light chain of anti-BRIL SRP2070 fab antibody / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.065002 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MEAPAQLLFL LLLWLPSSRA MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSG TDFTLSINSV ETEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN F YPKDINVK ...String:
MEAPAQLLFL LLLWLPSSRA MDIVLTQSPA TLSVTPGDRV SLSCRASQSV SNYLHWYQQK SHESPRLLIK YASQSISGIP SRFSGSGSG TDFTLSINSV ETEDFGMYFC QQSNSWPLTF GAGTKLELRR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN F YPKDINVK WKIDGSERQN GVLNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNEC

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Macromolecule #3: Heavy chain of anti-BRIL SRP2070 fab antibody

MacromoleculeName: Heavy chain of anti-BRIL SRP2070 fab antibody / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.421154 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MEAPAQLLFL LLLWLPSSRA MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKA TLIVDTSSST AFMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS G SSVTLGCL ...String:
MEAPAQLLFL LLLWLPSSRA MQIQLQQSGP ELVKPGASVK ISCKASGYTF TDFYINWMKQ RPGQGLEWIG WIFPGSGNTH YNEKFKGKA TLIVDTSSST AFMQLNSLTS EDSAVYFCTR PVSYYYDFDY WGQGTTLTVS SAKTTAPSVY PLAPVCGDTS G SSVTLGCL VKGYFPEPVT LTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVTSSTWPSQ SITCNVAHPA SSTKVDKKIE PR GCLEVLF QGPGHHHHHH HHSAWSHPQF EKGGGSGGGG SGGSAWSHPQ FEK

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Macromolecule #4: (R)-Tolvaptan

MacromoleculeName: (R)-Tolvaptan / type: ligand / ID: 4 / Number of copies: 1 / Formula: A1IT8
Molecular weightTheoretical: 448.941 Da

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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: 50.0 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: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 380888
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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