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Yorodumi- PDB-8hsv: The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 8hsv | ||||||
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Title | The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Arrestin | ||||||
Function / homology | Function and homology information localization / V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding ...localization / V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Golgi Associated Vesicle Biogenesis / MAP2K and MAPK activation / Ub-specific processing proteases / positive regulation of smooth muscle cell apoptotic process / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / traversing start control point of mitotic cell cycle / clathrin adaptor activity / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / regulation of G protein-coupled receptor signaling pathway / heart valve development / receptor serine/threonine kinase binding / arrestin family protein binding / G protein-coupled receptor internalization / positive regulation of vascular associated smooth muscle cell migration / response to morphine / peroxisome proliferator activated receptor binding / SUMO transferase activity / Thrombin signalling through proteinase activated receptors (PARs) / negative regulation of protein processing / response to steroid hormone / NEDD8 ligase activity / response to iron ion / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / ventricular septum development / mitogen-activated protein kinase kinase binding / cellular response to antibiotic / endocardial cushion morphogenesis / positive regulation of Rho protein signal transduction / clathrin binding / : / positive regulation of muscle cell differentiation / negative regulation of Notch signaling pathway / stress fiber assembly / cellular response to alkaloid / regulation of protein catabolic process / blood vessel development / cardiac septum morphogenesis / ligase activity / pseudopodium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of interleukin-6 production / negative regulation of DNA damage response, signal transduction by p53 class mediator / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of receptor internalization / phototransduction / response to magnesium ion / cellular response to organic cyclic compound / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of cell cycle / clathrin-coated pit / negative regulation of protein ubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / insulin-like growth factor receptor binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / visual perception / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / GTPase activator activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of protein export from nucleus / negative regulation of protein phosphorylation / proteolysis involved in protein catabolic process / response to cocaine / ubiquitin binding / positive regulation of protein ubiquitination / G protein-coupled receptor binding / nuclear estrogen receptor binding / phosphoprotein binding / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Yun, Y. / Yoon, H.J. / Choi, Y. / Lee, H.H. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2023 Title: GPCR targeting of E3 ubiquitin ligase MDM2 by inactive beta-arrestin. Authors: Yun, Y. / Yoon, H.J. / Jeong, Y. / Choi, Y. / Jang, S. / Chung, K.Y. / Lee, H.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8hsv.cif.gz | 162.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hsv.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 8hsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hs/8hsv ftp://data.pdbj.org/pub/pdb/validation_reports/hs/8hsv | HTTPS FTP |
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-Related structure data
Related structure data | 8hstC 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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Unit cell |
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-Components
#1: Protein | Mass: 46505.809 Da / Num. of mol.: 2 / Mutation: C59V,C125S,C140S,C150V,C242V,C251V,C269S 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: 1907.858 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) References: UniProt: D3ZVH5, RING-type E3 ubiquitin transferase #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 1M ammonium sulfate, 0.1M HEPES pH 9.5, 5mM n-dodecyl-b-iminodipropionic acid, monosodium salt |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2022 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→50 Å / Num. obs: 25258 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.035 / Rrim(I) all: 0.113 / Χ2: 0.599 / Net I/σ(I): 5.3 / Num. measured all: 266391 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→40.34 Å / Cross valid method: FREE R-VALUE / Phase error: 21 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→40.34 Å
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Refine LS restraints |
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LS refinement shell |
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