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- PDB-8hsv: The structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide -

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Basic information

Entry
Database: PDB / ID: 8hsv
TitleThe structure of rat beta-arrestin1 in complex with a rat Mdm2 peptide
Components
  • Beta-arrestin-1
  • peptide from E3 ubiquitin-protein ligase Mdm2
KeywordsSIGNALING PROTEIN / Arrestin
Function / homology
Function and homology information


: / V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway ...: / V2 vasopressin receptor binding / regulation of inositol trisphosphate biosynthetic process / alpha-1A adrenergic receptor binding / follicle-stimulating hormone receptor binding / TGFBR3 regulates TGF-beta signaling / sensory perception of touch / G alpha (s) signalling events / alpha-1B adrenergic receptor binding / follicle-stimulating hormone signaling pathway / protein phosphorylated amino acid binding / Lysosome Vesicle Biogenesis / angiotensin receptor binding / Golgi Associated Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / MAP2K and MAPK activation / cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / traversing start control point of mitotic cell cycle / negative regulation of interleukin-8 production / Clathrin-mediated endocytosis / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of signal transduction by p53 class mediator / regulation of G protein-coupled receptor signaling pathway / heart valve development / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / G protein-coupled receptor internalization / arrestin family protein binding / positive regulation of vascular associated smooth muscle cell migration / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of protein processing / SUMO transferase activity / response to iron ion / NEDD8 ligase activity / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / Thrombin signalling through proteinase activated receptors (PARs) / response to steroid hormone / cellular response to antibiotic / ventricular septum development / endocardial cushion morphogenesis / response to morphine / mitogen-activated protein kinase kinase binding / clathrin binding / positive regulation of muscle cell differentiation / cellular response to alkaloid / positive regulation of Rho protein signal transduction / regulation of postsynaptic neurotransmitter receptor internalization / cardiac septum morphogenesis / blood vessel development / stress fiber assembly / ligase activity / regulation of protein catabolic process / : / negative regulation of DNA damage response, signal transduction by p53 class mediator / pseudopodium / negative regulation of interleukin-6 production / response to magnesium ion / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of receptor internalization / cellular response to UV-C / cellular response to estrogen stimulus / blood vessel remodeling / cellular response to actinomycin D / negative regulation of Notch signaling pathway / phototransduction / protein localization to nucleus / ribonucleoprotein complex binding / protein autoubiquitination / clathrin-coated pit / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of cell cycle / insulin-like growth factor receptor binding / transcription repressor complex / negative regulation of protein ubiquitination / positive regulation of mitotic cell cycle / GTPase activator activity / regulation of heart rate / proteolysis involved in protein catabolic process / ubiquitin binding / positive regulation of protein export from nucleus / positive regulation of protein ubiquitination / nuclear estrogen receptor binding / phosphoprotein binding / response to cocaine / G protein-coupled receptor binding / establishment of protein localization / cellular response to gamma radiation / protein destabilization / negative regulation of ERK1 and ERK2 cascade / cellular response to growth factor stimulus
Similarity search - Function
Immunoglobulin-like - #640 / 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 ...Immunoglobulin-like - #640 / 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 / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / Arrestin-like, C-terminal / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Immunoglobulin E-set / Zinc finger, RING/FYVE/PHD-type / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2 / Beta-arrestin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
E: peptide from E3 ubiquitin-protein ligase Mdm2
B: Beta-arrestin-1
F: peptide from E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3089
Polymers96,8274
Non-polymers4805
Water1,58588
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.673, 80.673, 173.555
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Beta-arrestin-1 / 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: Protein/peptide peptide from E3 ubiquitin-protein ligase Mdm2


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 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 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

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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: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3-3.0510.50.84412460.930.9820.2740.8870.412100
3.05-3.1110.60.83512940.9150.9770.2690.8780.405100
3.11-3.1710.70.68712150.9420.9850.220.7210.409100
3.17-3.2310.80.56713280.9490.9870.1810.5950.428100
3.23-3.310.50.45311770.9680.9920.1470.4770.421100
3.3-3.3810.60.38513190.9610.990.1240.4050.425100
3.38-3.4610.20.29412330.9820.9950.0970.310.447100
3.46-3.569.80.22212670.990.9970.0750.2340.448100
3.56-3.669.30.18912930.9940.9980.0660.20.491100
3.66-3.789.80.14912400.9960.9990.050.1570.504100
3.78-3.9110.60.14812580.9950.9990.0470.1550.523100
3.91-4.0711.20.12112650.9970.9990.0380.1270.544100
4.07-4.2611.20.09712950.9980.9990.030.1010.586100
4.26-4.4811.10.07512400.99810.0240.0790.697100
4.48-4.76110.06512810.99910.0210.0680.746100
4.76-5.13110.06512310.99910.020.0680.762100
5.13-5.6410.80.06812640.9980.9990.0220.0710.755100
5.64-6.4610.30.0712650.99810.0230.0740.716100
6.46-8.139.50.05512770.99810.0190.0580.89100
8.13-5011.40.04712700.99910.0150.0491.29399.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2085 1338 5.3 %
Rwork0.176 --
obs0.1786 25251 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5954 0 0 88 6042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016065
X-RAY DIFFRACTIONf_angle_d1.3158223
X-RAY DIFFRACTIONf_dihedral_angle_d9.696808
X-RAY DIFFRACTIONf_chiral_restr0.068941
X-RAY DIFFRACTIONf_plane_restr0.011065
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.22871250.21962380X-RAY DIFFRACTION95
3.11-3.230.2651020.18842458X-RAY DIFFRACTION96
3.23-3.380.18171080.17642392X-RAY DIFFRACTION96
3.38-3.560.17712180.1672294X-RAY DIFFRACTION91
3.56-3.780.17551500.16192395X-RAY DIFFRACTION94
3.78-4.070.19531320.16112383X-RAY DIFFRACTION95
4.07-4.480.19091260.15042402X-RAY DIFFRACTION95
4.48-5.130.1971230.14752380X-RAY DIFFRACTION95
5.13-6.450.29051150.22842428X-RAY DIFFRACTION95
6.46-40.340.2641390.20232401X-RAY DIFFRACTION94

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