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Yorodumi- PDB-8gp3: Structure of beta-arrestin1 in complex with a phosphopeptide corr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8gp3 | ||||||
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Title | Structure of beta-arrestin1 in complex with a phosphopeptide corresponding to the human C-X-C chemokine receptor type 4, CXCR4 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GPCR / Arrestin | ||||||
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 / C-X-C motif chemokine 12 receptor activity / regulation of viral process / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / positive regulation of vascular wound healing ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / sensory perception of touch / C-X-C motif chemokine 12 receptor activity / regulation of viral process / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / positive regulation of vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / positive regulation of mesenchymal stem cell migration / angiotensin receptor binding / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / myosin light chain binding / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / positive regulation of smooth muscle cell apoptotic process / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / C-C chemokine binding / Signaling by ROBO receptors / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of chemotaxis / positive regulation of chemotaxis / cellular response to organonitrogen compound / Formation of definitive endoderm / positive regulation of dendrite extension / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / anchoring junction / Thrombin signalling through proteinase activated receptors (PARs) / Chemokine receptors bind chemokines / dendritic cell chemotaxis / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / positive regulation of oligodendrocyte differentiation / stress fiber assembly / negative regulation of Notch signaling pathway / epithelial cell development / cell leading edge / pseudopodium / cellular response to cytokine stimulus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / detection of temperature stimulus involved in sensory perception of pain / small molecule binding / negative regulation of interleukin-6 production / regulation of calcium ion transport / positive regulation of receptor internalization / phototransduction / Binding and entry of HIV virion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / clathrin-coated pit / negative regulation of protein ubiquitination / cardiac muscle contraction / insulin-like growth factor receptor binding / visual perception / neurogenesis / GTPase activator activity / cell chemotaxis / negative regulation of protein phosphorylation / response to activity / ubiquitin binding / positive regulation of protein ubiquitination / G protein-coupled receptor binding / G protein-coupled receptor activity / nuclear estrogen receptor binding / calcium-mediated signaling / phosphoprotein binding / brain development / neuron migration / response to virus / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / endocytosis / cellular response to xenobiotic stimulus / late endosome 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: 4.8 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 | 8gp3.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gp3.ent.gz | 214.4 KB | Display | PDB format |
PDBx/mmJSON format | 8gp3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/8gp3 ftp://data.pdbj.org/pub/pdb/validation_reports/gp/8gp3 | HTTPS FTP |
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-Related structure data
Related structure data | 34188MC 8go8C 8gocC 8gooC 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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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: Protein/peptide | Mass: 2380.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61073 #3: 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) #4: 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) 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 | ||||||||||||||||||||||||||||||
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 FIELDBright-field microscopy / 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: 49.3 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 5637 |
Image scans | Movie frames/image: 40 |
-Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 3236193 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53387 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8GO8 |