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- PDB-8hst: The structure of rat beta-arrestin1 -

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Basic information

Entry
Database: PDB / ID: 8hst
TitleThe structure of rat beta-arrestin1
ComponentsBeta-arrestin-1Arrestin
KeywordsSIGNALING PROTEIN / 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 / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / angiotensin receptor binding ...V2 vasopressin receptor binding / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / Activation of SMO / 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 / negative regulation of interleukin-8 production / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / regulation of G protein-coupled receptor signaling pathway / arrestin family protein binding / G protein-coupled receptor internalization / Thrombin signalling through proteinase activated receptors (PARs) / mitogen-activated protein kinase kinase binding / positive regulation of Rho protein signal transduction / clathrin binding / stress fiber assembly / negative regulation of Notch signaling pathway / 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 / phototransduction / clathrin-coated pit / negative regulation of protein ubiquitination / insulin-like growth factor receptor binding / visual perception / GTPase activator activity / negative regulation of protein phosphorylation / positive regulation of protein ubiquitination / G protein-coupled receptor binding / nuclear estrogen receptor binding / phosphoprotein binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of ERK1 and ERK2 cascade / endocytosis / protein transport / positive regulation of peptidyl-serine phosphorylation / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / postsynaptic membrane / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 / response to xenobiotic stimulus / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / signaling receptor binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsYun, Y. / Yoon, H.J. / Choi, Y. / Lee, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: 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
DepositionDec 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-1
B: Beta-arrestin-1


Theoretical massNumber of molelcules
Total (without water)93,0122
Polymers93,0122
Non-polymers00
Water2,630146
1
A: Beta-arrestin-1


Theoretical massNumber of molelcules
Total (without water)46,5061
Polymers46,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-arrestin-1


Theoretical massNumber of molelcules
Total (without water)46,5061
Polymers46,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.285, 72.484, 116.388
Angle α, β, γ (deg.)90.00, 98.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-arrestin-1 / Arrestin / Arrestin beta-1


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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 5% (w/v) PEG 8000, 100mM Imidazole/ Hydrochloric acid pH 8.0, 100mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 11, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 57442 / % possible obs: 99.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.984 / Χ2: 0.052 / Net I/σ(I): 6.8 / Num. measured all: 201036
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.66-2.713.30.36827410.442195.4
2.71-2.763.40.36527940.453198.3
2.76-2.813.50.36429320.46199.4
2.81-2.873.50.31428180.468199.9
2.87-2.933.60.25529260.4931100
2.93-33.60.21428880.509199.9
3-3.073.50.18428480.5331100
3.07-3.153.50.16429350.591100
3.15-3.253.40.13428540.5981100
3.25-3.353.10.11228570.7071100
3.35-3.473.20.10129040.7411100
3.47-3.613.50.09128810.8791100
3.61-3.773.70.0928810.9251100
3.77-3.973.70.07728981.0651100
3.97-4.223.70.07128731.2081100
4.22-4.553.70.06329201.427199.8
4.55-53.60.06128481.582199.9
5-5.733.50.06128711.456199.7
5.73-7.213.10.06129061.37199.9
7.21-503.80.05828672.126199.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXv1.19.2refinement
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→38.62 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2479 1455 4.92 %
Rwork0.1836 --
obs0.1868 29545 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→38.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5758 0 0 146 5904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095875
X-RAY DIFFRACTIONf_angle_d1.1327961
X-RAY DIFFRACTIONf_dihedral_angle_d8.083783
X-RAY DIFFRACTIONf_chiral_restr0.062914
X-RAY DIFFRACTIONf_plane_restr0.0091029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.760.26391240.17472739X-RAY DIFFRACTION98
2.76-2.870.21891380.16162797X-RAY DIFFRACTION100
2.87-30.23751360.16162824X-RAY DIFFRACTION100
3-3.160.25471550.1932798X-RAY DIFFRACTION100
3.16-3.350.25761560.19342766X-RAY DIFFRACTION100
3.35-3.610.25581440.18632815X-RAY DIFFRACTION100
3.61-3.970.29681540.2042810X-RAY DIFFRACTION100
3.97-4.550.24731560.17432824X-RAY DIFFRACTION100
4.55-5.730.22761520.17252812X-RAY DIFFRACTION100
5.73-38.620.21651400.19842905X-RAY DIFFRACTION100

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