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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 / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of Rho protein signal transduction ...angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / arrestin family protein binding / G protein-coupled receptor internalization / enzyme inhibitor activity / 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 / positive regulation of receptor internalization / pseudopodium / negative regulation of interleukin-6 production / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / 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 / protein ubiquitination / positive regulation of protein phosphorylation / lysosomal membrane / Golgi membrane / ubiquitin protein ligase binding / chromatin / regulation of transcription by RNA polymerase II / 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-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 2, 2022-
Header (metadata) releaseSep 14, 2022-
Map releaseSep 14, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14223.png

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)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 140 pix.
= 179.2 Å		1.28 Å/pix.
x 140 pix.
= 179.2 Å		1.28 Å/pix.
x 140 pix.
= 179.2 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: 0.26
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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Mask #1

Fileemd_14223_msk_1.map
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Additional map: #1

Fileemd_14223_additional_1.map
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Half map: #2

Fileemd_14223_half_map_1.map
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Half map: #1

Fileemd_14223_half_map_2.map
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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
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
FSC plot (resolution estimation)

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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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