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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 receptor
    • Protein or peptide: AVP
    • Protein or peptide: Arrestin2
    • Protein or peptide: ScFv30
KeywordsG-protein coupled receptor V2 receptor Arrestin 2 Vasopressin / 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 / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / hemostasis / positive regulation of systemic arterial blood pressure ...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 / TGFBR3 regulates TGF-beta signaling / Activation of SMO / hemostasis / positive regulation of systemic arterial blood pressure / 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 / negative regulation of NF-kappaB transcription factor activity / positive regulation of Rho protein signal transduction / Golgi Associated Vesicle Biogenesis / stress fiber assembly / negative regulation of Notch signaling pathway / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / endocytic vesicle / activation of adenylate cyclase activity / clathrin-coated pit / cellular response to hormone stimulus / positive regulation of vasoconstriction / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / response to cytokine / G protein-coupled receptor binding / peptide binding / Signaling by high-kinase activity BRAF mutants / clathrin-coated endocytic vesicle membrane / MAP2K and MAPK activation / cytoplasmic vesicle membrane / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / 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 / protein transport / Cargo recognition for clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / 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 / nuclear body / Ub-specific processing proteases / endosome / protein ubiquitination / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / endoplasmic reticulum / 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing 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
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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

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Half map: #1

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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 receptor
    • 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 / 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

UniProtKB: Vasopressin V2 receptor

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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

UniProtKB: Beta-arrestin-1

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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
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
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
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

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

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Atomic model buiding 1

Initial model
PDB IDChain

7kh0

chain_id: A, source_name: PDB, initial_model_type: experimental model

4jqi

chain_id: C, source_name: PDB, initial_model_type: experimental model
Output model

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

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