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- EMDB-14223: Structure of the V2 receptor Cter-arrestin2-ScFv30 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14223
TitleStructure of the V2 receptor Cter-arrestin2-ScFv30 complex
Map data
Sample
  • Complex: Ternary complex of the Cterminal portion of the V2 receptor with arrestin2 and ScfV30
    • Protein or peptide: V2R Cter
    • 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


angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / 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 / Golgi Associated Vesicle Biogenesis ...angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / 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 / Golgi Associated Vesicle Biogenesis / stress fiber assembly / positive regulation of Rho protein signal transduction / pseudopodium / negative regulation of interleukin-6 production / positive regulation of receptor internalization / enzyme inhibitor activity / negative regulation of Notch signaling pathway / Activated NOTCH1 Transmits Signal to the Nucleus / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Signaling by high-kinase activity BRAF mutants / G protein-coupled receptor binding / MAP2K and MAPK activation / endocytic vesicle membrane / 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 / Cargo recognition for clathrin-mediated endocytosis / Signaling by BRAF and RAF1 fusions / Clathrin-mediated endocytosis / protein transport / Thrombin signalling through proteinase activated receptors (PARs) / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / 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 / Ub-specific processing proteases / protein ubiquitination / nuclear body / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 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-beta-arrestin1 ternary complex.
Authors: Bous J / Fouillen A / Orcel H / Trapani S / Cong X / Fontanel S / Saint-Paul J / Lai-Kee-Him J / Urbach S / Sibille N / Sounier R / Granier S / Mouillac B / Bron P
History
DepositionFeb 2, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_14223.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.28 Å
Density
Contour LevelBy AUTHOR: 0.26
Minimum - Maximum-0.5140041 - 0.89467126
Average (Standard dev.)0.018550336 (±0.045059245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 179.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ternary complex of the Cterminal portion of the V2 receptor with ...

EntireName: Ternary complex of the Cterminal portion of the V2 receptor with arrestin2 and ScfV30
Components
  • Complex: Ternary complex of the Cterminal portion of the V2 receptor with arrestin2 and ScfV30
    • Protein or peptide: V2R Cter
    • Protein or peptide: Arrestin2
    • Protein or peptide: ScFv30

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Supramolecule #1: Ternary complex of the Cterminal portion of the V2 receptor with ...

SupramoleculeName: Ternary complex of the Cterminal portion of the 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: V2R Cter

MacromoleculeName: V2R Cter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.780248 KDa
Recombinant expressionOrganism: Insect expression vector pBlueBacmsGCA1 (others)
SequenceString:
E(SEP)C(TPO)(TPO)A(SEP)(SEP)(SEP)L AKD

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Macromolecule #2: Arrestin2

MacromoleculeName: Arrestin2 / type: protein_or_peptide / ID: 2 / 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 #3: ScFv30

MacromoleculeName: ScFv30 / type: protein_or_peptide / ID: 3 / 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
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kh0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27637
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Details: +SGD cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

4jqi


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7r0j:
Structure of the V2 receptor Cter-arrestin2-ScFv30 complex

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