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Yorodumi- PDB-8i0n: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8i0n | ||||||
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Title | Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C5a anaphylatoxin chemotactic receptor 1, C5aR1 (Local refine) | ||||||
Components |
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Keywords | SIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / Arrestin / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / G alpha (s) signalling events / alpha-1B adrenergic receptor binding ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / complement component C5a signaling pathway / presynapse organization / regulation of tau-protein kinase activity / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / complement component C5a receptor activity / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / response to peptidoglycan / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / sensory perception of chemical stimulus / positive regulation of smooth muscle cell apoptotic process / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / complement receptor mediated signaling pathway / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / positive regulation of neutrophil chemotaxis / Thrombin signalling through proteinase activated receptors (PARs) / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / positive regulation of macrophage chemotaxis / stress fiber assembly / negative regulation of Notch signaling pathway / amyloid-beta clearance / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of interleukin-6 production / positive regulation of receptor internalization / activation of phospholipase C activity / phototransduction / positive regulation of vascular endothelial growth factor production / cellular defense response / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / Peptide ligand-binding receptors / neutrophil chemotaxis / secretory granule membrane / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / positive regulation of epithelial cell proliferation / G protein-coupled receptor binding / Regulation of Complement cascade / astrocyte activation / G protein-coupled receptor activity / nuclear estrogen receptor binding / phosphoprotein binding / microglial cell activation / mRNA transcription by RNA polymerase II / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / cognition / endocytosis / positive regulation of angiogenesis / chemotaxis / protein transport / apical part of cell / positive regulation of peptidyl-serine phosphorylation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / postsynaptic membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / basolateral plasma membrane / regulation of apoptotic process / negative regulation of neuron apoptotic process / transmembrane transporter binding / dendritic spine / positive regulation of MAPK cascade / transcription coactivator activity / positive regulation of ERK1 and ERK2 cascade / protein ubiquitination / endosome / defense response to Gram-positive bacterium / immune response / response to xenobiotic stimulus / inflammatory response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 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: 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 | 8i0n.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i0n.ent.gz | 190.7 KB | Display | PDB format |
PDBx/mmJSON format | 8i0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/8i0n ftp://data.pdbj.org/pub/pdb/validation_reports/i0/8i0n | HTTPS FTP |
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-Related structure data
Related structure data | 35104MC 8go8C 8gocC 8gooC 8gp3C 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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1 |
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-Components
#1: Protein | Mass: 47088.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Arrb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29066 #2: Antibody | 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 | 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 | Mass: 2698.340 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21730 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
Component |
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Molecular weight | Value: 0.19 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. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 56 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 6212 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4304237 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80437 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8GO8 |