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- EMDB-36110: Structure of basal beta-arrestin2 -

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Basic information

Entry
Database: EMDB / ID: EMD-36110
TitleStructure of basal beta-arrestin2
Map data
Sample
  • Complex: beta-arrestin2 in complex with Fab6
    • Complex: beta-arrestin2
      • Protein or peptide: Beta-arrestin-2
    • Complex: Fab6
      • Protein or peptide: Fab6 light chain
      • Protein or peptide: Fab6 heavy chain
KeywordsGPCR / 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 / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / angiotensin receptor binding / protein kinase B binding / positive regulation of cardiac muscle cell differentiation / WNT5A-dependent internalization of FZD4 / MAP2K and MAPK activation / Ub-specific processing proteases / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of toll-like receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / negative regulation of interleukin-12 production / regulation of G protein-coupled receptor signaling pathway / positive regulation of calcium ion transport / arrestin family protein binding / G protein-coupled receptor internalization / type 1 angiotensin receptor binding / positive regulation of epithelial cell apoptotic process / Thrombin signalling through proteinase activated receptors (PARs) / mitogen-activated protein kinase binding / response to morphine / adult walking behavior / negative regulation of interleukin-1 beta production / positive regulation of DNA biosynthetic process / negative regulation of release of cytochrome c from mitochondria / positive regulation of receptor internalization / negative regulation of smooth muscle cell apoptotic process / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / endocytic vesicle / negative regulation of tumor necrosis factor production / positive regulation of collagen biosynthetic process / D1 dopamine receptor binding / negative regulation of canonical NF-kappaB signal transduction / clathrin-coated pit / positive regulation of glial cell proliferation / 14-3-3 protein binding / negative regulation of protein ubiquitination / transforming growth factor beta receptor signaling pathway / negative regulation of protein phosphorylation / cell chemotaxis / G protein-coupled receptor binding / regulation of protein phosphorylation / modulation of chemical synaptic transmission / receptor internalization / circadian rhythm / endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / protein transport / positive regulation of peptidyl-serine phosphorylation / cytoplasmic vesicle / basolateral plasma membrane / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / molecular adaptor activity / dendritic spine / positive regulation of ERK1 and ERK2 cascade / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / protein ubiquitination / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / protein domain specific binding / signaling receptor binding / glutamatergic synapse / ubiquitin protein ligase binding / protein-containing complex binding / positive regulation of gene expression / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 3, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36110.png

Downloads & links

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Map

FileDownload / File: emd_36110.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 256 pix.
= 316.083 Å		1.23 Å/pix.
x 256 pix.
= 316.083 Å		1.23 Å/pix.
x 256 pix.
= 316.083 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2347 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-1.3791598 - 1.9680638
Average (Standard dev.)0.00006074891 (±0.019752316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 316.0832 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_36110_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36110_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : beta-arrestin2 in complex with Fab6

EntireName: beta-arrestin2 in complex with Fab6
Components
  • Complex: beta-arrestin2 in complex with Fab6
    • Complex: beta-arrestin2
      • Protein or peptide: Beta-arrestin-2
    • Complex: Fab6
      • Protein or peptide: Fab6 light chain
      • Protein or peptide: Fab6 heavy chain

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Supramolecule #1: beta-arrestin2 in complex with Fab6

SupramoleculeName: beta-arrestin2 in complex with Fab6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: beta-arrestin2

SupramoleculeName: beta-arrestin2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Fab6

SupramoleculeName: Fab6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Beta-arrestin-2

MacromoleculeName: Beta-arrestin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 44.490906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GTRVFKKSSP NCKLTVYLGK RDFVDHLDKV DPVDGVVLVD PDYLKDRKVF VTLTCAFRYG REDLDVLGLS FRKDLFIATY QAFPPMPNP PRPPTRLQDR LLKKLGQHAH PFFFTIPQNL PCSVTLQPGP EDTGKACGVD FEIRAFCAKS IEEKSHKRNS V RLIIRKVQ ...String:
GTRVFKKSSP NCKLTVYLGK RDFVDHLDKV DPVDGVVLVD PDYLKDRKVF VTLTCAFRYG REDLDVLGLS FRKDLFIATY QAFPPMPNP PRPPTRLQDR LLKKLGQHAH PFFFTIPQNL PCSVTLQPGP EDTGKACGVD FEIRAFCAKS IEEKSHKRNS V RLIIRKVQ FAPETPGPQP SAETTRHFLM SDRRSLHLEA SLDKELYYHG EPLNVNVHVT NNSAKTVKKI RVSVRQYADI CL FSTAQYK CPVAQLEQDD QVSPSSTFCK VYTITPLLSD NREKRGLALD GQLKHEDTNL ASSTIVKEGA NKEVLGILVS YRV KVKLVV SRGGDVSVEL PFVLMHPKPH DHITLPRPQS APREIDIPVD TNLIEFDTNY ATDDDIVFED FARLRLK

UniProtKB: Beta-arrestin-2

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Macromolecule #2: Fab6 light chain

MacromoleculeName: Fab6 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.356607 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSKYDGLITF GQGTKVA

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Macromolecule #3: Fab6 heavy chain

MacromoleculeName: Fab6 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.636962 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SEVQLVESGG GLVQPGGSLR LSCAASGFNF SSSYIHWVRQ APGKGLEWVA SISSYYGYTS YADSVKGRFT ISADTSKNTA YLQMNSLRA EDTAVYYCAR QGYYYNSYMQ GALDYWGQGT LVTVSS

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Particle selectionNumber selected: 7887274
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8goc

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Number images used: 506938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8goc


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

PDB-8j9k:
Structure of basal beta-arrestin2

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