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- PDB-8j9k: Structure of basal beta-arrestin2 -

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Basic information

Entry
Database: PDB / ID: 8j9k
TitleStructure of basal beta-arrestin2
Components
  • Beta-arrestin-2
  • Fab6 heavy chain
  • Fab6 light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / positive regulation of synaptic transmission, dopaminergic / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events ...type 2A serotonin receptor binding / platelet activating factor receptor binding / postsynaptic signal transduction / negative regulation of opioid receptor signaling pathway / positive regulation of opioid receptor signaling pathway / positive regulation of synaptic transmission, dopaminergic / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / G alpha (s) signalling events / follicle-stimulating hormone signaling pathway / alpha-1B adrenergic receptor binding / WNT5A-dependent internalization of FZD4 / positive regulation of cardiac muscle cell differentiation / protein kinase B binding / angiotensin receptor binding / Ub-specific processing proteases / MAP2K and MAPK activation / desensitization of G protein-coupled receptor signaling pathway / negative regulation of toll-like receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of interleukin-12 production / type 1 angiotensin receptor binding / regulation of G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / G protein-coupled receptor internalization / arrestin family protein binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of epithelial cell apoptotic process / mitogen-activated protein kinase binding / adult walking behavior / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of DNA biosynthetic process / negative regulation of interleukin-1 beta production / response to morphine / negative regulation of release of cytochrome c from mitochondria / detection of temperature stimulus involved in sensory perception of pain / negative regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-6 production / positive regulation of collagen biosynthetic process / positive regulation of receptor internalization / positive regulation of glial cell proliferation / negative regulation of tumor necrosis factor production / endocytic vesicle / D1 dopamine receptor binding / clathrin-coated pit / 14-3-3 protein binding / negative regulation of protein ubiquitination / negative regulation of canonical NF-kappaB signal transduction / transforming growth factor beta receptor signaling pathway / cell chemotaxis / G protein-coupled receptor binding / circadian rhythm / modulation of chemical synaptic transmission / receptor internalization / endocytosis / protein transport / cytoplasmic vesicle / basolateral plasma membrane / molecular adaptor activity / dendritic spine / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / postsynaptic membrane / transcription by RNA polymerase II / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / postsynaptic density / protein ubiquitination / G protein-coupled receptor signaling pathway / signaling receptor binding / protein domain specific binding / ubiquitin protein ligase binding / positive regulation of gene expression / protein-containing complex binding / glutamatergic synapse / enzyme binding / identical protein binding / nucleus / plasma membrane / 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 speciesRattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 3, 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 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Beta-arrestin-2
B: Fab6 light chain
D: Fab6 heavy chain


Theoretical massNumber of molelcules
Total (without water)69,4843
Polymers69,4843
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-2 / Arrestin beta-2


Mass: 44490.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29067
#2: Antibody Fab6 light chain


Mass: 11356.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab6 heavy chain


Mass: 13636.962 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
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-arrestin2 in complex with Fab6COMPLEXall0RECOMBINANT
2beta-arrestin2COMPLEX#11RECOMBINANT
3Fab6COMPLEX#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Rattus norvegicus (Norway rat)10116
33Mus musculus (house mouse)10090
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
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 defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3.3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 7887274
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 506938 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8GOC

8goc


Accession code: 8GOC / Source name: PDB / Type: experimental model

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