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- PDB-1g4r: CRYSTAL STRUCTURE OF BOVINE BETA-ARRESTIN 1 -

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Basic information

Entry
Database: PDB / ID: 1g4r
TitleCRYSTAL STRUCTURE OF BOVINE BETA-ARRESTIN 1
ComponentsBETA-ARRESTIN 1
KeywordsSIGNALING PROTEIN / Signal transduction / G-proteins / G-protein coupled receptors
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, SHARP / Resolution: 2.2 Å
AuthorsSchubert, C. / Han, M.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of beta-arrestin at 1.9 A: possible mechanism of receptor binding and membrane Translocation.
Authors: Han, M. / Gurevich, V.V. / Vishnivetskiy, S.A. / Sigler, P.B. / Schubert, C.
History
DepositionOct 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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: BETA-ARRESTIN 1


Theoretical massNumber of molelcules
Total (without water)44,3101
Polymers44,3101
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.806, 77.806, 157.099
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 BETA-ARRESTIN 1


Mass: 44309.578 Da / Num. of mol.: 1 / Fragment: TRUNCATION MUTANT: 1-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PTRC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17870
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.05 Å3/Da / Density % sol: 59.31 %
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein11or 7mg/ml
20.1 M11NaCl
320 mMTris-HCl11
41 mMEDTA11
510 mMdithiothreitol11
65 %glycerol11
718-20 %PEG150012
80.8 M12MgCl2
90.1 MTris-HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: May 24, 2000 / Details: mirrors and Si(111)
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→34 Å / Num. all: 29214 / Num. obs: 54018 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Biso Wilson estimate: 47.7 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 4.6 / Net I/σ(I): 10.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4041 / Rsym value: 50 / % possible all: 81.5
Reflection
*PLUS
Num. obs: 27920 / % possible obs: 94.7 % / Redundancy: 9.6 % / Num. measured all: 267488
Reflection shell
*PLUS
% possible obs: 79.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SHARP
Starting model: 1CF1

1cf1


Resolution: 2.2→32.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1571954.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 5218 9.9 %RANDOM
Rwork0.238 ---
all0.262 52464 --
obs0.238 52464 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.45 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 64.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å22.33 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 0 102 2900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it5.391.5
X-RAY DIFFRACTIONc_mcangle_it7.222
X-RAY DIFFRACTIONc_scbond_it7.862
X-RAY DIFFRACTIONc_scangle_it9.942.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.392 410 9.2 %
Rwork0.355 4041 -
obs--81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor Rfree: 0.267
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 64.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / % reflection Rfree: 9.2 % / Rfactor Rwork: 0.355

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