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

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Basic information

Entry
Database: PDB / ID: 8ja3
TitleStructure of beta-arrestin1 in complex with C3aRpp
Components
  • Beta-arrestin-1
  • C3a anaphylatoxin chemotactic receptor
  • Fab30 heavy chain
  • Fab30 light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / 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 / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway ...V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / 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 / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / complement component C5a receptor activity / Lysosome Vesicle Biogenesis / angiotensin receptor binding / Golgi Associated Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / MAP2K and MAPK activation / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / negative regulation of interleukin-8 production / Clathrin-mediated endocytosis / complement receptor mediated signaling pathway / regulation of G protein-coupled receptor signaling pathway / G protein-coupled receptor internalization / arrestin family protein binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of neutrophil chemotaxis / blood circulation / Thrombin signalling through proteinase activated receptors (PARs) / azurophil granule membrane / response to morphine / mitogen-activated protein kinase kinase binding / clathrin binding / positive regulation of Rho protein signal transduction / stress fiber assembly / positive regulation of macrophage chemotaxis / pseudopodium / negative regulation of interleukin-6 production / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of receptor internalization / positive regulation of vascular endothelial growth factor production / negative regulation of Notch signaling pathway / phototransduction / Purinergic signaling in leishmaniasis infection / specific granule membrane / clathrin-coated pit / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / GTPase activator activity / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / phosphoprotein binding / G protein-coupled receptor binding / calcium-mediated signaling / 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 angiogenesis / chemotaxis / protein transport / positive regulation of protein phosphorylation / positive regulation of cytosolic calcium ion concentration / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / G alpha (i) signalling events / basolateral plasma membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / regulation of apoptotic process / dendritic spine / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / postsynaptic membrane / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / postsynaptic density / endosome / protein ubiquitination / G protein-coupled receptor signaling pathway / inflammatory response / response to xenobiotic stimulus / 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 / cytosol
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsMaharana, J. / Sarma, P. / Yadav, M.K. / Chami, M. / Banerjee, R. / Shukla, A.K.
Funding support India, 4items
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, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Beta-arrestin-1
U: C3a anaphylatoxin chemotactic receptor
I: Fab30 heavy chain
M: Fab30 light chain
A: Beta-arrestin-1
V: C3a anaphylatoxin chemotactic receptor
H: Fab30 heavy chain
L: Fab30 light chain


Theoretical massNumber of molelcules
Total (without water)181,0138
Polymers181,0138
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Beta-arrestin-1 / Arrestin beta-1


Mass: 40075.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066
#2: Protein/peptide C3a anaphylatoxin chemotactic receptor / C3AR / C3a-R


Mass: 1484.165 Da / Num. of mol.: 2 / Fragment: C-terminal tail / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16581
#3: Antibody Fab30 heavy chain


Mass: 25512.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Antibody Fab30 light chain


Mass: 23435.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1beta-arrestin1 in complex with C3aRppCOMPLEXall0RECOMBINANT
2beta-arrestin-1COMPLEX#11RECOMBINANT
3Fab30 Heavy ChainCOMPLEX#31RECOMBINANT
4Fab30 Light ChainCOMPLEX#41RECOMBINANT
5Phosphopeptide derived from the C-terminal tail of C3aR receptor (C3aRpp)COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
25
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Rattus norvegicus (Norway rat)10116
24Mus musculus (house mouse)10090
33Mus musculus (house mouse)10090
45Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
34Escherichia coli (E. coli)562
43Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2300 mMSodium chlorideNaCl1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 46000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 13438
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARC4classification
13cryoSPARC43D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 8834633
3D reconstructionResolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164339 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8GO8

8go8


Accession code: 8GO8 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 79.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00418985
ELECTRON MICROSCOPYf_angle_d0.762412234
ELECTRON MICROSCOPYf_chiral_restr0.04691389
ELECTRON MICROSCOPYf_plane_restr0.00691558
ELECTRON MICROSCOPYf_dihedral_angle_d10.88771270

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