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- PDB-8i0z: Structure of beta-arrestin2 in complex with a phosphopeptide corr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8i0z | ||||||
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Title | Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine) | ||||||
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![]() | SIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / angiotensin receptor binding / response to peptidoglycan / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / sensory perception of chemical stimulus / complement receptor mediated signaling pathway ...complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / complement component C5a receptor activity / angiotensin receptor binding / response to peptidoglycan / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / sensory perception of chemical stimulus / complement receptor mediated signaling pathway / G protein-coupled receptor internalization / positive regulation of neutrophil chemotaxis / positive regulation of macrophage chemotaxis / amyloid-beta clearance / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / : / endocytic vesicle / positive regulation of vascular endothelial growth factor production / cellular defense response / clathrin-coated pit / phosphatidylinositol binding / Peptide ligand-binding receptors / neutrophil chemotaxis / secretory granule membrane / Regulation of Complement cascade / positive regulation of epithelial cell proliferation / G protein-coupled receptor activity / astrocyte activation / microglial cell activation / mRNA transcription by RNA polymerase II / receptor internalization / cognition / positive regulation of angiogenesis / chemotaxis / protein transport / apical part of cell / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / immune response / Neutrophil degranulation / signal transduction / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.33 Å | ||||||
![]() | Maharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K. | ||||||
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![]() | ![]() 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: ![]() Title: Structure of beta-arrestin in complex with a phosphopeptide Authors: Maharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 311.5 KB | Display | ![]() |
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PDB format | ![]() | 246.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 62.8 KB | Display | |
Data in CIF | ![]() | 93 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 35114MC ![]() 8go8C ![]() 8gocC ![]() 8gooC ![]() 8gp3C ![]() 8i0nC ![]() 8i0qC ![]() 8i10C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 25512.354 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 23435.064 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Protein/peptide | Mass: 2698.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Value: 0.28 MDa / Experimental value: YES | |||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | |||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||||||||||||
Vitrification | Instrument: 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
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 holder | Cryogen: NITROGEN |
Image recording | Electron dose: 51 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8614 |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4012616 | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38206 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8GOO Accession code: 8GOO / Source name: PDB / Type: experimental model |