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- PDB-3p2d: Crystal structure of arrestin-3 reveals the basis of the differen... -

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Basic information

Entry
Database: PDB / ID: 3p2d
TitleCrystal structure of arrestin-3 reveals the basis of the difference in receptor binding between two non-visual subtypes
ComponentsBeta-arrestin-2Arrestin beta 2
KeywordsSIGNALING PROTEIN / arrestin / signal transduction / cytosol
Function / homology
Function and homology information


angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / G protein-coupled receptor binding ...angiotensin receptor binding / desensitization of G protein-coupled receptor signaling pathway / inositol hexakisphosphate binding / G protein-coupled receptor internalization / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / endocytic vesicle / clathrin-coated pit / phosphatidylinositol binding / G protein-coupled receptor binding / receptor internalization / protein transport / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / signal transduction / nucleus / 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
Beta-arrestin-2 / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSpiller, B.W. / Gurevich, V.V. / Zhan, X. / Gimenez, L.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Arrestin-3 Reveals the Basis of the Difference in Receptor Binding Between Two Non-visual Subtypes.
Authors: Zhan, X. / Gimenez, L.E. / Gurevich, V.V. / Spiller, B.W.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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-2
B: Beta-arrestin-2


Theoretical massNumber of molelcules
Total (without water)88,4712
Polymers88,4712
Non-polymers00
Water0
1
A: Beta-arrestin-2


Theoretical massNumber of molelcules
Total (without water)44,2351
Polymers44,2351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-arrestin-2


Theoretical massNumber of molelcules
Total (without water)44,2351
Polymers44,2351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.177, 73.323, 201.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-arrestin-2 / Arrestin beta 2 / Arrestin beta-2 / Arrestin-3


Mass: 44235.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB2 / Plasmid: pTrcHis2B / Production host: Escherichia coli (E. coli) / References: UniProt: P32120-2, UniProt: P32120*PLUS

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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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM HEPES, 675mM Na/K tartrate, pH 7.5. , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: 0.97914 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 22556 / Num. obs: 20910 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 3→3.11 Å / % possible all: 92.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1g4r

1g4r


Resolution: 3→35.364 Å / SU ML: 0.4 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2864 1092 5.23 %random, throughout
Rwork0.2189 ---
all0.2225 ---
obs0.2225 20879 92.57 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.854 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.9867 Å20 Å20 Å2
2--8.7842 Å2-0 Å2
3---5.2025 Å2
Refinement stepCycle: LAST / Resolution: 3→35.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5611 0 0 0 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115737
X-RAY DIFFRACTIONf_angle_d1.5317771
X-RAY DIFFRACTIONf_dihedral_angle_d18.4522191
X-RAY DIFFRACTIONf_chiral_restr0.096878
X-RAY DIFFRACTIONf_plane_restr0.011010
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.1350.35621240.30422454X-RAY DIFFRACTION92
3.135-3.30010.33891310.27012466X-RAY DIFFRACTION94
3.3001-3.50670.34511310.25742490X-RAY DIFFRACTION94
3.5067-3.77720.30891520.24182454X-RAY DIFFRACTION94
3.7772-4.15680.30041620.22582455X-RAY DIFFRACTION94
4.1568-4.75710.25191090.17122487X-RAY DIFFRACTION93
4.7571-5.98870.26061620.2122460X-RAY DIFFRACTION92
5.9887-35.36670.27341210.21342521X-RAY DIFFRACTION88

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