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- PDB-8i0z: Structure of beta-arrestin2 in complex with a phosphopeptide corr... -

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Basic information

Entry
Database: PDB / ID: 8i0z
TitleStructure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine)
Components
  • Beta-arrestin-2
  • C5a anaphylatoxin chemotactic receptor 1
  • 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


complement component C5a signaling pathway / presynapse organization / complement component C5a receptor activity / response to peptidoglycan / angiotensin receptor binding / sensory perception of chemical stimulus / desensitization of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / G protein-coupled receptor internalization / inositol hexakisphosphate binding ...complement component C5a signaling pathway / presynapse organization / complement component C5a receptor activity / response to peptidoglycan / angiotensin receptor binding / sensory perception of chemical stimulus / desensitization of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / G protein-coupled receptor internalization / inositol hexakisphosphate binding / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / phosphatidylinositol-3,4,5-trisphosphate binding / amyloid-beta clearance / positive regulation of vascular endothelial growth factor production / positive regulation of receptor internalization / endocytic vesicle / cellular defense response / clathrin-coated pit / neutrophil chemotaxis / astrocyte activation / phosphatidylinositol binding / secretory granule membrane / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / mRNA transcription by RNA polymerase II / microglial cell activation / G protein-coupled receptor activity / receptor internalization / cognition / positive regulation of angiogenesis / chemotaxis / apical part of cell / protein transport / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / immune response / inflammatory response / Neutrophil degranulation / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Formyl peptide receptor-related / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Anaphylatoxin chemotactic receptor, C3a/C5a1/C5a2 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Formyl peptide receptor-related / 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
C5a anaphylatoxin chemotactic receptor 1 / 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: 4.33 Å
AuthorsMaharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)IPA/2020/000405 India
Citation
Journal: Mol Cell / Year: 2023
Title: Structural snapshots uncover a key phosphorylation motif in GPCRs driving β-arrestin activation.
Authors: Jagannath Maharana / Parishmita Sarma / Manish K Yadav / Sayantan Saha / Vinay Singh / Shirsha Saha / Mohamed Chami / Ramanuj Banerjee / Arun K Shukla /
Abstract: Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent ...Agonist-induced GPCR phosphorylation is a key determinant for the binding and activation of β-arrestins (βarrs). However, it is not entirely clear how different GPCRs harboring divergent phosphorylation patterns impart converging active conformation on βarrs leading to broadly conserved functional responses such as desensitization, endocytosis, and signaling. Here, we present multiple cryo-EM structures of activated βarrs in complex with distinct phosphorylation patterns derived from the carboxyl terminus of different GPCRs. These structures help identify a P-X-P-P type phosphorylation motif in GPCRs that interacts with a spatially organized K-K-R-R-K-K sequence in the N-domain of βarrs. Sequence analysis of the human GPCRome reveals the presence of this phosphorylation pattern in a large number of receptors, and its contribution in βarr activation is demonstrated by targeted mutagenesis experiments combined with an intrabody-based conformational sensor. Taken together, our findings provide important structural insights into the ability of distinct GPCRs to activate βarrs through a significantly conserved mechanism.
#1: Journal: Mol.Cell / Year: 2023
Title: Structure of beta-arrestin in complex with a phosphopeptide
Authors: Maharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K.
History
DepositionJan 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update
Revision 1.2Oct 23, 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

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Assembly

Deposited unit
A: Beta-arrestin-2
B: Beta-arrestin-2
C: Beta-arrestin-2
D: Fab30 Heavy Chain
E: Fab30 Light Chain
G: C5a anaphylatoxin chemotactic receptor 1
H: Fab30 Heavy Chain
L: Fab30 Light Chain
M: Fab30 Heavy Chain
N: Fab30 Light Chain
U: C5a anaphylatoxin chemotactic receptor 1
V: C5a anaphylatoxin chemotactic receptor 1


Theoretical massNumber of molelcules
Total (without water)296,59012
Polymers296,59012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
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.: 3
Mutation: C17G,C60V,L69V,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.: 3
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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein/peptide C5a anaphylatoxin chemotactic receptor 1 / C5a anaphylatoxin chemotactic receptor / C5a-R / C5aR


Mass: 2698.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21730
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-IDSourceDetails
1Peptide4 bound beta-arrestin2 in complex with Fab30COMPLEXall0MULTIPLE SOURCES
2beta-arrestin 2COMPLEX#11RECOMBINANT
3Fab30COMPLEX#2-#31RECOMBINANT
4C5a anaphylatoxin chemotactic receptor 1 phosphopeptideCOMPLEX#41SYNTHETICChemically synthesized
Molecular weightValue: 0.28 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
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

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 / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 51 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8614
Image scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC3.3.1CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARC3.3.1classification
13cryoSPARC3.3.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 4012616
3D reconstructionResolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38206 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 8GOO

8goo


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

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