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- PDB-8go9: Structure of beta-arrestin2 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: PDB / ID: 8go9
TitleStructure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human Atypical chemokine receptor 2, ACKR2 (D6R)
Components
  • Atypical chemokine receptor 2
  • Beta-arrestin-2
  • 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


angiotensin receptor binding / chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / C-C chemokine binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / Chemokine receptors bind chemokines / scavenger receptor activity / phosphatidylinositol-3,4,5-trisphosphate binding ...angiotensin receptor binding / chemokine receptor activity / desensitization of G protein-coupled receptor signaling pathway / C-C chemokine receptor activity / C-C chemokine binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / Chemokine receptors bind chemokines / scavenger receptor activity / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / cell chemotaxis / actin filament / calcium-mediated signaling / recycling endosome / receptor internalization / protein transport / positive regulation of cytosolic calcium ion concentration / nuclear membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / intracellular signal transduction / immune response / inflammatory response / external side of plasma membrane / intracellular membrane-bounded organelle / signal transduction / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
CXC chemokine receptor 4/atypical chemokine receptor 2 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Chemokine receptor family / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...CXC chemokine receptor 4/atypical chemokine receptor 2 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Chemokine receptor family / 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 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
Atypical chemokine receptor 2 / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Mus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsMaharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K.
Funding support India, 4items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Science and Engineering Research Board (SERB)CRG/2022/002646 India
Science and Engineering Research Board (SERB)SPR/2020/000408 India
Department of Biotechnology (DBT, India)IA/S/20/1/504916 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
DepositionAug 24, 2022Deposition 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
A: Beta-arrestin-2
B: Fab30 Heavy Chain
C: Fab30 Light Chain
D: Fab30 Heavy Chain
E: Fab30 Light Chain
F: Beta-arrestin-2
G: Atypical chemokine receptor 2
H: Atypical chemokine receptor 2


Theoretical massNumber of molelcules
Total (without water)197,0368
Polymers197,0368
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 / Arrestin-3


Mass: 47217.676 Da / Num. of mol.: 2
Mutation: C17G,C66V,L69C,C126S,C141L,C151V,C243V,C252V,C270S,L278F,S280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ARRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32120
#2: 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)
#3: 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)
#4: Protein/peptide Atypical chemokine receptor 2 / C-C chemokine receptor D6 / Chemokine receptor CCR-10 / Chemokine receptor CCR-9 / Chemokine- ...C-C chemokine receptor D6 / Chemokine receptor CCR-10 / Chemokine receptor CCR-9 / Chemokine-binding protein 2 / Chemokine-binding protein D6


Mass: 2352.668 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00590
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
1Peptide bound beta-arrestin2 in complex with Fab30COMPLEXall0MULTIPLE SOURCES
2beta-arrestin2COMPLEX#11RECOMBINANT
3Fab30COMPLEX#2-#32RECOMBINANT
4Atypical chemokine receptor 2COMPLEX#43SYNTHETIC
Molecular weightValue: 0.19 MDa / Experimental value: YES
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bos taurus (domestic cattle)9913
23Mus musculus (house mouse)10090
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia 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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K / Details: Blotted for 3 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 10028
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7Cootmodel fitting
11cryoSPARC3.3.1classification
12cryoSPARC3.3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1827629
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 94497 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 5TV1

5tv1


Accession code: 5TV1 / Source name: PDB / Type: experimental model

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