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- EMDB-14221: Structure of the AVP-V2R-arrestin2-ScFv30 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14221
TitleStructure of the AVP-V2R-arrestin2-ScFv30 complex
Map data
Sample
  • Complex: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30
    • Protein or peptide: Vasopressin V2 receptorVasopressin receptor 2
    • Protein or peptide: AVP
    • Protein or peptide: Arrestin2
    • Protein or peptide: ScFv30
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 / Activation of SMO / positive regulation of systemic arterial blood pressure / hemostasis / 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 / Activation of SMO / positive regulation of systemic arterial blood pressure / hemostasis / telencephalon development / negative regulation of interleukin-8 production / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / positive regulation of intracellular signal transduction / Lysosome Vesicle Biogenesis / positive regulation of Rho protein signal transduction / Golgi Associated Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / stress fiber assembly / negative regulation of Notch signaling pathway / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / cellular response to hormone stimulus / insulin-like growth factor receptor binding / activation of adenylate cyclase activity / visual perception / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / G protein-coupled receptor binding / response to cytokine / peptide binding / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / MAP2K and MAPK activation / cytoplasmic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / 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 / Signaling by BRAF and RAF1 fusions / Thrombin signalling through proteinase activated receptors (PARs) / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / nuclear body / Ub-specific processing proteases / endosome / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / lysosomal membrane / negative regulation of cell population proliferation / Golgi membrane / ubiquitin protein ligase binding / positive regulation of cell population proliferation / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.73 Å
AuthorsBous J / Fouillen A / Trapani S / Granier S / Mouillac B / Bron P
Funding support France, 2 items
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, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14221.png

Downloads & links

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Map

FileDownload / File: emd_14221.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 220 pix.
= 281.6 Å		1.28 Å/pix.
x 220 pix.
= 281.6 Å		1.28 Å/pix.
x 220 pix.
= 281.6 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.28 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.271
Minimum - Maximum-0.8178623 - 1.1559271
Average (Standard dev.)-0.001271722 (±0.034730162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14221_msk_1.map
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Additional map: #1

Fileemd_14221_additional_1.map
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Half map: #2

Fileemd_14221_half_map_1.map
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Half map: #1

Fileemd_14221_half_map_2.map
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Sample components

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Entire : Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30

EntireName: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30
Components
  • Complex: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30
    • Protein or peptide: Vasopressin V2 receptorVasopressin receptor 2
    • Protein or peptide: AVP
    • Protein or peptide: Arrestin2
    • Protein or peptide: ScFv30

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Supramolecule #1: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30

SupramoleculeName: Ternary complex of the AVP-V2 receptor with arrestin2 and ScfV30
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vasopressin V2 receptor

MacromoleculeName: Vasopressin V2 receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.532367 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCA1 (others)
SequenceString: GPDYKDDDDA ASTTSAVPGH PSLPSLPSQS SQERPLDTRD PLLARAELAL LSIVFVAVAL SNGLVLAALA RRGRRGHWAP IHVFIGHLC LADLAVALFQ VLPQLAWKAT DRFRGPDALC RAVKYLQMVG MYASSYMILA MTLDRHRAIC RPMLAYRHGS G AHWNRPVL ...String:
GPDYKDDDDA ASTTSAVPGH PSLPSLPSQS SQERPLDTRD PLLARAELAL LSIVFVAVAL SNGLVLAALA RRGRRGHWAP IHVFIGHLC LADLAVALFQ VLPQLAWKAT DRFRGPDALC RAVKYLQMVG MYASSYMILA MTLDRHRAIC RPMLAYRHGS G AHWNRPVL VAWAFSLLLS LPQLFIFAQR NVEGGSGVTD CWACFAEPWG RRTYVTWIAL MVFVAPTLGI AACQVLIFRE IH ASLVPGP SERPGGRRRG RRTGSPGEGA HVSAAVAKTV RMTLVIVVVY VLCWAPFFLV QLWAAWDPEA PLEGAPFVLL MLL ASLNSC TNPWIYASFS SSVSSELRSL LCCARGRTPP SLGPQDE(SEP)C(TPO) (TPO)A(SEP)(SEP)(SEP)LAKDT SS

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Macromolecule #2: AVP

MacromoleculeName: AVP / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.086248 KDa
SequenceString:
CYFQNCPRG(NH2)

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Macromolecule #3: Arrestin2

MacromoleculeName: Arrestin2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.164609 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGASWSHPQF EKGGGSGGGS GGSSAWSHPQ FEKLEVLFQG PASGDKGTRV FKKASPNGKL TVYLGKRDFV DHIDLVDPVD GVVLVDPEY LKERRVYVTL TCAFRYGRED LDVLGLTFRK DLFVANVQSF PPAPEDKKPL TRLQERLIKK LGEHAYPFTF E IPPNLPCS ...String:
MGASWSHPQF EKGGGSGGGS GGSSAWSHPQ FEKLEVLFQG PASGDKGTRV FKKASPNGKL TVYLGKRDFV DHIDLVDPVD GVVLVDPEY LKERRVYVTL TCAFRYGRED LDVLGLTFRK DLFVANVQSF PPAPEDKKPL TRLQERLIKK LGEHAYPFTF E IPPNLPCS VTLQPGPEDT GKACGVDYEV KAFCAENLEE KIHKRNSVRL VIRKVQYAPE RPGPQPTAET TRQFLMSDKP LH LEASLDK EIYYHGEPIS VNVHVTNNTN KTVKKIKISV RQYADICLFN TAQYKCPVAM EEADDTVAPS STFCKVYTLT PFL ANNREK RGLALDGKLK HEDTNLASST LLREGANREI LGIIVSYKVK VKLVVSRGGL LGDLASSDVA VELPFTLMHP KPKE EPPHR EVPENETPVD TNLIELDTN

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Macromolecule #4: ScFv30

MacromoleculeName: ScFv30 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 30.070027 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCA1 (others)
SequenceString: AMGDIQMTQS PSSLSASVGD RVTITCRASQ SVSSAVAWYQ QKPGKAPKLL IYSASSLYSG VPSRFSGSRS GTDFTLTISS LQPEDFATY YCQQYKYVPV TFGCGTKVEI KGTTAASGSS GGSSSGAEVQ LVESGGGLVQ PGGSLRLSCA ASGFNVYSSS I HWVRQAPG ...String:
AMGDIQMTQS PSSLSASVGD RVTITCRASQ SVSSAVAWYQ QKPGKAPKLL IYSASSLYSG VPSRFSGSRS GTDFTLTISS LQPEDFATY YCQQYKYVPV TFGCGTKVEI KGTTAASGSS GGSSSGAEVQ LVESGGGLVQ PGGSLRLSCA ASGFNVYSSS I HWVRQAPG KCLEWVASIS SYYGYTYYAD SVKGRFTISA DTSKNTAYLQ MNSLRAEDTA VYYCARSRQF WYSGLDYWGQ GT LVTVSSA AADDDDKAGW SHPQFEKGGG SGGGSGGGSW SHPQFEK

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 130000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 14080 / Average exposure time: 1.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4595394
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kh0

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Details: +SGD cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8296
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7kh0

chain_id: A

4jqi

chain_id: C
Output model

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

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