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- PDB-1jsy: Crystal structure of bovine arrestin-2 -

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Basic information

Entry
Database: PDB / ID: 1jsy
TitleCrystal structure of bovine arrestin-2
ComponentsBovine arrestin-2 (full length)
KeywordsSIGNALING PROTEIN / Nonvisual arrestins / beta-arrestins / desensitization / endocytosis / down-regulation
Function / homology
Function and homology information


MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis ...MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / clathrin heavy chain binding / clathrin coat of coated pit / Ub-specific processing proteases / desensitization of G protein-coupled receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / inositol hexakisphosphate binding / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / G protein-coupled receptor internalization / acetylcholine receptor binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / negative regulation of Notch signaling pathway / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / small molecule binding / positive regulation of receptor internalization / visual perception / G protein-coupled receptor binding / receptor internalization / protein transport / ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / positive regulation of protein phosphorylation / signal transduction / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #840 / 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 ...Immunoglobulin-like - #840 / 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 / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMilano, S.K. / Pace, H.C. / Kim, Y.M. / Brenner, C. / Benovic, J.L.
CitationJournal: Biochemistry / Year: 2002
Title: Scaffolding functions of arrestin-2 revealed by crystal structure and mutagenesis.
Authors: Milano, S.K. / Pace, H.C. / Kim, Y.M. / Brenner, C. / Benovic, J.L.
History
DepositionAug 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bovine arrestin-2 (full length)


Theoretical massNumber of molelcules
Total (without water)47,2021
Polymers47,2021
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.952, 78.952, 158.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Bovine arrestin-2 (full length)


Mass: 47201.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pTrcHisB (without the His tag) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-lysS / References: UniProt: P17870
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 3.03 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: magnesium formate, polypropylene glycol 400, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.5 mg/mlprotein1drop
25 mMHEPES1droppH7.2
30.5 mMEDTA1drop
462.5 mM1dropNaCl
575 mMmagnesium formate1drop
620 %PEG4001drop
7150 mMmagnesium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001 / Details: mirrors
RadiationMonochromator: Bent, triangular Si(111) (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.9→19 Å / Num. all: 13592 / Num. obs: 13476 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.1 % / Biso Wilson estimate: 70.4 Å2 / Rsym value: 7.4 / Net I/σ(I): 11.9
Reflection shellResolution: 2.9→3 Å / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 19 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.318

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CF1; CHAIN B

1cf1


Resolution: 2.9→19 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 341288.37 / Isotropic thermal model: Group / Cross valid method: THROUGHOUT / σ(F): 1.5 / Stereochemistry target values: Mlf
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1320 10.2 %Random
Rwork0.23 ---
all0.23 13476 --
obs0.227 13136 97.4 %-
Solvent computationSolvent model: FLAT / Bsol: 27.7387 Å2 / ksol: 0.290823 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.09 Å28.12 Å20 Å2
2---4.09 Å20 Å2
3---8.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.9→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2829 0 0 76 2905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 193 9.6 %
Rwork0.325 1821 -
obs-2014 93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Refinement
*PLUS
Lowest resolution: 19 Å / Num. reflection Rfree: 1314 / Rfactor all: 0.23 / Rfactor obs: 0.2298 / Rfactor Rfree: 0.2385 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Rfactor Rfree: 0.323 / Rfactor Rwork: 0.325

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