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Yorodumi- PDB-8goo: Structure of beta-arrestin2 in complex with a phosphopeptide corr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8goo | ||||||
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Title | Structure of beta-arrestin2 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GPCR / Arrestin | ||||||
Function / homology | Function and homology information angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / receptor internalization ...angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / receptor internalization / protein transport / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / signal transduction / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Maharana, J. / Sarma, P. / Yadav, M.K. / Banerjee, R. / Shukla, A.K. | ||||||
Funding support | India, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8goo.cif.gz | 384.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8goo.ent.gz | 313.2 KB | Display | PDB format |
PDBx/mmJSON format | 8goo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8goo_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8goo_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8goo_validation.xml.gz | 71.4 KB | Display | |
Data in CIF | 8goo_validation.cif.gz | 104.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/8goo ftp://data.pdbj.org/pub/pdb/validation_reports/go/8goo | HTTPS FTP |
-Related structure data
Related structure data | 34178MC 8go8C 8gocC 8gp3C 8i0nC 8i0qC 8i0zC 8i10C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 47217.676 Da / Num. of mol.: 3 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 (cattle) / Gene: ARRB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P32120 #2: Antibody | 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 | 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 | Mass: 2698.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) 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 |
-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 | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 283.15 K / Details: Blotted for 3 seconds before plunging. |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4012616 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.4 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: 8GOC Accession code: 8GOC / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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