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- PDB-7r0c: Structure of the AVP-V2R-arrestin2-ScFv30 complex -

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Basic information

Entry
Database: PDB / ID: 7r0c
TitleStructure of the AVP-V2R-arrestin2-ScFv30 complex
Components
  • AVP
  • Arrestin2
  • ScFv30
  • Vasopressin V2 receptor
KeywordsMEMBRANE PROTEIN / G-protein coupled receptor V2 receptor Arrestin 2 Vasopressin
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 / angiotensin receptor binding / hemostasis / TGFBR3 regulates TGF-beta signaling / Activation of SMO / telencephalon development ...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 / angiotensin receptor binding / hemostasis / TGFBR3 regulates TGF-beta signaling / Activation of SMO / telencephalon development / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / positive regulation of vasoconstriction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / endocytic vesicle / negative regulation of Notch signaling pathway / enzyme inhibitor activity / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / clathrin-coated pit / response to cytokine / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / clathrin-coated endocytic vesicle membrane / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / endosome / Ub-specific processing proteases / protein ubiquitination / nuclear body / G protein-coupled receptor signaling pathway / Golgi membrane / negative regulation of cell population proliferation / lysosomal membrane / positive regulation of cell population proliferation / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Vasopressin V2 receptor / Vasopressin receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.73 Å
AuthorsBous, J. / Fouillen, A. / Trapani, S. / Granier, S. / Mouillac, B. / Bron, P.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE11-0014 France
Foundation for Medical Research (France)DEQ20150331736 France
CitationJournal: Sci Adv / Year: 2022
Title: Structure of the vasopressin hormone-V2 receptor-β-arrestin1 ternary complex.
Authors: Julien Bous / Aurélien Fouillen / Hélène Orcel / Stefano Trapani / Xiaojing Cong / Simon Fontanel / Julie Saint-Paul / Joséphine Lai-Kee-Him / Serge Urbach / Nathalie Sibille / Rémy ...Authors: Julien Bous / Aurélien Fouillen / Hélène Orcel / Stefano Trapani / Xiaojing Cong / Simon Fontanel / Julie Saint-Paul / Joséphine Lai-Kee-Him / Serge Urbach / Nathalie Sibille / Rémy Sounier / Sébastien Granier / Bernard Mouillac / Patrick Bron /
Abstract: Arrestins interact with G protein-coupled receptors (GPCRs) to stop G protein activation and to initiate key signaling pathways. Recent structural studies shed light on the molecular mechanisms ...Arrestins interact with G protein-coupled receptors (GPCRs) to stop G protein activation and to initiate key signaling pathways. Recent structural studies shed light on the molecular mechanisms involved in GPCR-arrestin coupling, but whether this process is conserved among GPCRs is poorly understood. Here, we report the cryo-electron microscopy active structure of the wild-type arginine-vasopressin V2 receptor (V2R) in complex with β-arrestin1. It reveals an atypical position of β-arrestin1 compared to previously described GPCR-arrestin assemblies, associated with an original V2R/β-arrestin1 interface involving all receptor intracellular loops. Phosphorylated sites of the V2R carboxyl terminus are clearly identified and interact extensively with the β-arrestin1 N-lobe, in agreement with structural data obtained with chimeric or synthetic systems. Overall, these findings highlight a notable structural variability among GPCR-arrestin signaling complexes.
History
DepositionFeb 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
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Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vasopressin V2 receptor
B: AVP
C: Arrestin2
D: ScFv30


Theoretical massNumber of molelcules
Total (without water)119,8534
Polymers119,8534
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Extensive pharmacology, Ns-EM
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 41532.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AVPR2, ADHR, DIR, DIR3, V2R
Production host: Insect expression vector pBlueBacmsGCA1 (others)
References: UniProt: P30518
#2: Protein/peptide AVP


Mass: 1086.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Arrestin2


Mass: 47164.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P49407
#4: Antibody ScFv30


Mass: 30070.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Insect expression vector pBlueBacmsGCA1 (others)
Has ligand of interestN
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: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Insect expression vector pBlueBacmsGCA1s
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 1 sec. / Electron dose: 52 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 14080

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM software
IDNameVersionCategory
2Topazparticle selection
3RELION3.1.2particle selection
11PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4595394
3D reconstructionResolution: 4.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8296 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
17KH0

7kh0

A7KH01
24JQI

4jqi

C4JQI2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047066
ELECTRON MICROSCOPYf_angle_d0.7319627
ELECTRON MICROSCOPYf_dihedral_angle_d7.414988
ELECTRON MICROSCOPYf_chiral_restr0.0471101
ELECTRON MICROSCOPYf_plane_restr0.0051204

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