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- EMDB-36124: Structure of beta-arrestin1 in complex with C3aRpp -

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Basic information

Entry
Database: EMDB / ID: EMD-36124
TitleStructure of beta-arrestin1 in complex with C3aRpp
Map data
Sample
  • Complex: beta-arrestin1 in complex with C3aRpp
    • Complex: beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: Fab30 Heavy Chain
      • Protein or peptide: Fab30 heavy chain
    • Complex: Fab30 Light Chain
      • Protein or peptide: Fab30 light chain
    • Complex: Phosphopeptide derived from the C-terminal tail of C3aR receptor (C3aRpp)
      • Protein or peptide: C3a anaphylatoxin chemotactic receptor
KeywordsGPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V2 vasopressin receptor binding / complement component C3a receptor activity / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / sensory perception of touch / G alpha (s) signalling events / regulation of inositol trisphosphate biosynthetic process / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding ...V2 vasopressin receptor binding / complement component C3a receptor activity / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / sensory perception of touch / G alpha (s) signalling events / regulation of inositol trisphosphate biosynthetic process / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / complement component C5a receptor activity / alpha-1B adrenergic receptor binding / Lysosome Vesicle Biogenesis / angiotensin receptor binding / AP-2 adaptor complex binding / Ub-specific processing proteases / MAP2K and MAPK activation / Golgi Associated Vesicle Biogenesis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / negative regulation of interleukin-8 production / regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / G protein-coupled receptor internalization / arrestin family protein binding / positive regulation of neutrophil chemotaxis / mitogen-activated protein kinase kinase binding / blood circulation / Thrombin signalling through proteinase activated receptors (PARs) / azurophil granule membrane / response to morphine / clathrin binding / stress fiber assembly / positive regulation of macrophage chemotaxis / positive regulation of Rho protein signal transduction / pseudopodium / negative regulation of interleukin-6 production / positive regulation of vascular endothelial growth factor production / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / phototransduction / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Purinergic signaling in leishmaniasis infection / specific granule membrane / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / Peptide ligand-binding receptors / Regulation of Complement cascade / nuclear estrogen receptor binding / positive regulation of protein ubiquitination / phosphoprotein binding / calcium-mediated signaling / G protein-coupled receptor binding / G protein-coupled receptor activity / negative regulation of ERK1 and ERK2 cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / endocytosis / positive regulation of protein phosphorylation / positive regulation of angiogenesis / chemotaxis / protein transport / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (i) signalling events / regulation of apoptotic process / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / molecular adaptor activity / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / postsynaptic membrane / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / endosome / positive regulation of MAPK cascade / postsynaptic density / protein ubiquitination / G protein-coupled receptor signaling pathway / response to xenobiotic stimulus / inflammatory response / signaling receptor binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / glutamatergic synapse / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane
Similarity search - Function
C3a anaphylatoxin chemotactic receptor / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / 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 ...C3a anaphylatoxin chemotactic receptor / Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Formyl peptide receptor-related / 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
Beta-arrestin-1 / C3a anaphylatoxin chemotactic receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsMaharana J / Sarma P / Yadav MK / Chami M / Banerjee R / Shukla AK
Funding support India, 4 items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Department of Biotechnology (DBT, India)IA/S/20/1/504916 India
Science and Engineering Research Board (SERB)CRG/2022/002646 India
Science and Engineering Research Board (SERB)SPR/2020/000408 India
CitationJournal: Science / Year: 2024
Title: Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors.
Authors: Jagannath Maharana / Fumiya K Sano / Parishmita Sarma / Manish K Yadav / Longhan Duan / Tomasz M Stepniewski / Madhu Chaturvedi / Ashutosh Ranjan / Vinay Singh / Sayantan Saha / Gargi ...Authors: Jagannath Maharana / Fumiya K Sano / Parishmita Sarma / Manish K Yadav / Longhan Duan / Tomasz M Stepniewski / Madhu Chaturvedi / Ashutosh Ranjan / Vinay Singh / Sayantan Saha / Gargi Mahajan / Mohamed Chami / Wataru Shihoya / Jana Selent / Ka Young Chung / Ramanuj Banerjee / Osamu Nureki / Arun K Shukla /
Abstract: β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor ...β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor activation and phosphorylation. Here, we present seven cryo-electron microscopy structures of βarrs either in the basal state, activated by the muscarinic receptor subtype 2 (M2R) through its third intracellular loop, or activated by the βarr-biased decoy D6 receptor (D6R). Combined with biochemical, cellular, and biophysical experiments, these structural snapshots allow the visualization of atypical engagement of βarrs with 7TMRs and also reveal a structural transition in the carboxyl terminus of βarr2 from a β strand to an α helix upon activation by D6R. Our study provides previously unanticipated molecular insights into the structural and functional diversity encoded in 7TMR-βarr complexes with direct implications for exploring novel therapeutic avenues.
History
DepositionMay 5, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36124.png

Downloads & links

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Map

FileDownload / File: emd_36124.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 256 pix.
= 365.261 Å		1.43 Å/pix.
x 256 pix.
= 365.261 Å		1.43 Å/pix.
x 256 pix.
= 365.261 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.044
Minimum - Maximum-0.033745587 - 2.0371735
Average (Standard dev.)0.00040377086 (±0.013485957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 365.2608 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36124_half_map_1.map
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Half map: #1

Fileemd_36124_half_map_2.map
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Sample components

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Entire : beta-arrestin1 in complex with C3aRpp

EntireName: beta-arrestin1 in complex with C3aRpp
Components
  • Complex: beta-arrestin1 in complex with C3aRpp
    • Complex: beta-arrestin-1
      • Protein or peptide: Beta-arrestin-1
    • Complex: Fab30 Heavy Chain
      • Protein or peptide: Fab30 heavy chain
    • Complex: Fab30 Light Chain
      • Protein or peptide: Fab30 light chain
    • Complex: Phosphopeptide derived from the C-terminal tail of C3aR receptor (C3aRpp)
      • Protein or peptide: C3a anaphylatoxin chemotactic receptor

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Supramolecule #1: beta-arrestin1 in complex with C3aRpp

SupramoleculeName: beta-arrestin1 in complex with C3aRpp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: beta-arrestin-1

SupramoleculeName: beta-arrestin-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Fab30 Heavy Chain

SupramoleculeName: Fab30 Heavy Chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Fab30 Light Chain

SupramoleculeName: Fab30 Light Chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #5: Phosphopeptide derived from the C-terminal tail of C3aR receptor ...

SupramoleculeName: Phosphopeptide derived from the C-terminal tail of C3aR receptor (C3aRpp)
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 40.075152 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI ...String:
MGDKGTRVFK KASPNGKLTV YLGKRDFVDH IDLVDPVDGV VLVDPEYLKE RRVYVTLTCA FRYGREDLDV LGLTFRKDLF VANVQSFPP APEDKKPLTR LQERLIKKLG EHAYPFTFEI PPNLPCSVTL QPGPEDTGKA CGVDYEVKAF CAENLEEKIH K RNSVRLVI RKVQYAPERP GPQPTAETTR QFLMSDKPLH LEASLDKEIY YHGEPISVNV HVTNNTNKTV KKIKISVRQY AD ICLFNTA QYKCPVAMEE ADDTVAPSST FCKVYTLTPF LANNREKRGL ALDGKLKHED TNLASSTLLR EGANREILGI IVS YKVKVK LVVSRGGLLG DLASSDVAVE LPFTLMHPKP K

UniProtKB: Beta-arrestin-1

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Macromolecule #2: C3a anaphylatoxin chemotactic receptor

MacromoleculeName: C3a anaphylatoxin chemotactic receptor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.484165 KDa
SequenceString:
(SEP)EEL(TPO)R(SEP)(TPO)HC

UniProtKB: C3a anaphylatoxin chemotactic receptor

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Macromolecule #3: Fab30 heavy chain

MacromoleculeName: Fab30 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.512354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NVYSSSIHWV RQAPGKGLEW VASISSYYGY TYYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSRQFWYSG LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THHHHHHHH

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Macromolecule #4: Fab30 light chain

MacromoleculeName: Fab30 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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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

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
300.0 mMNaClSodium chloride
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number real images: 13438 / Average electron dose: 49.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 46000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 8834633
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8go8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 164339
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8go8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8ja3:
Structure of beta-arrestin1 in complex with C3aRpp

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