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- PDB-9uvw: Cryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL ... -

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Basic information

Entry
Database: PDB / ID: 9uvw
TitleCryo-EM structure of Vasopressin receptor 2 (V2R)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan, focused on receptor
ComponentsVasopressin V2 receptor,Soluble cytochrome b562
KeywordsMEMBRANE PROTEIN / GPCR / V2R / vasopressin / tolvaptan
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)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.89 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

Downloads & links

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Assembly

Deposited unit
A: Vasopressin V2 receptor,Soluble cytochrome b562
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0442
Polymers53,5951
Non-polymers4491
Water00
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,Soluble cytochrome b562 / V2R / AVPR V2 / Antidiuretic hormone receptor / Renal-type arginine vasopressin receptor / Cytochrome b-562


Mass: 53594.973 Da / Num. of mol.: 1 / Mutation: M243W/H338I/R342L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli (E. coli)
Gene: AVPR2, ADHR, DIR, DIR3, V2R, cybC / Production host: Homo sapiens (human) / References: UniProt: P30518, UniProt: P0ABE7
#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
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)-BRIL/anti BRIL SRP2070 Fab antibody complex with tolvaptan, focused on receptor
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
21Escherichia coli (E. coli)562
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: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 195895 / Symmetry type: POINT
RefinementResolution: 2.89→2.89 Å / Cor.coef. Fo:Fc: 0.788 / WRfactor Rwork: 0.404 / SU B: 20.383 / SU ML: 0.323 / Average fsc free: 0 / Average fsc overall: 0.6535 / Average fsc work: 0.6535 / ESU R: 0.323
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.4036 38163 -
all0.404 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 95.532 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.0122173
ELECTRON MICROSCOPYr_bond_other_d00.0162121
ELECTRON MICROSCOPYr_angle_refined_deg1.4861.7852969
ELECTRON MICROSCOPYr_angle_other_deg0.6491.7064823
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.865262
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.318424
ELECTRON MICROSCOPYr_dihedral_angle_3_deg13.66510330
ELECTRON MICROSCOPYr_dihedral_angle_6_deg11.5911079
ELECTRON MICROSCOPYr_chiral_restr0.0850.2344
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.022563
ELECTRON MICROSCOPYr_gen_planes_other0.0040.02547
ELECTRON MICROSCOPYr_nbd_refined0.2410.2489
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1640.21852
ELECTRON MICROSCOPYr_nbtor_refined0.1840.21058
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0660.21151
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1290.246
ELECTRON MICROSCOPYr_mcbond_it8.1148.8221060
ELECTRON MICROSCOPYr_mcbond_other8.0578.8251060
ELECTRON MICROSCOPYr_mcangle_it13.52415.8771318
ELECTRON MICROSCOPYr_mcangle_other13.53315.8831319
ELECTRON MICROSCOPYr_scbond_it9.42210.1971113
ELECTRON MICROSCOPYr_scbond_other9.41810.1921114
ELECTRON MICROSCOPYr_scangle_it16.0818.1651651
ELECTRON MICROSCOPYr_scangle_other16.07518.1591652
ELECTRON MICROSCOPYr_lrange_it26.128103.9358961
ELECTRON MICROSCOPYr_lrange_other26.127103.9318962
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
3-3.0780.97928780.97928780.2250.979
3.078-3.1620.65426990.65426990.2590.654
3.162-3.2540.62427310.62427310.3380.624
3.254-3.3540.57725720.57725720.4170.577
3.354-3.4640.50224890.50224890.5410.502
3.464-3.5850.45524050.45524050.610.455
3.585-3.720.42323760.42323760.6930.423
3.72-3.8720.37222190.37222190.7740.372
3.872-4.0440.3422650.3422650.8250.34
4.044-4.240.33520050.33520050.8680.335
4.24-4.4690.33919790.33919790.890.339
4.469-4.7390.32818920.32818920.90.328
4.739-5.0650.32917210.32917210.9140.329
5.065-5.470.33916730.33916730.890.339
5.47-5.9890.33614760.33614760.8360.336
5.989-6.6920.36113330.36113330.7940.361
6.692-7.7180.35612150.35612150.810.356
7.718-9.4330.329960.329960.8750.32
9.433-13.2540.2887900.2887900.9130.288
13.254-830.7534470.7534470.9320.753

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