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- PDB-5tv1: active arrestin-3 with inositol hexakisphosphate -

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Basic information

Entry
Database: PDB / ID: 5tv1
Titleactive arrestin-3 with inositol hexakisphosphate
ComponentsBeta-arrestin-2Arrestin beta 2
KeywordsSIGNALING PROTEIN
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 / receptor internalization ...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 / receptor internalization / protein transport / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / signal transduction / nucleus / cytoplasm
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 / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Beta-arrestin-2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChen, Q. / Gilbert, N.C. / Perry, N.A. / Vishniveteskiy, S. / Gurevich, V.V. / Iverson, T.M.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095633 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM077561 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109955 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY011500 United States
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of arrestin-3 activation and signaling.
Authors: Chen, Q. / Perry, N.A. / Vishnivetskiy, S.A. / Berndt, S. / Gilbert, N.C. / Zhuo, Y. / Singh, P.K. / Tholen, J. / Ohi, M.D. / Gurevich, E.V. / Brautigam, C.A. / Klug, C.S. / Gurevich, V.V. / Iverson, T.M.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Beta-arrestin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8606
Polymers44,2641
Non-polymers1,5965
Water79344
1
A: Beta-arrestin-2
hetero molecules

A: Beta-arrestin-2
hetero molecules

A: Beta-arrestin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,58018
Polymers132,7913
Non-polymers4,78915
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area10820 Å2
ΔGint-83 kcal/mol
Surface area49020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.575, 97.575, 76.938
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 44263.531 Da / Num. of mol.: 1 / Fragment: UNP residues 8-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ARRB2 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P32120
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM Succinate/Phosphate/Glycine pH 8.5 and 25% PEG 1500

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.4→37.03 Å / Num. obs: 15997 / % possible obs: 97 % / Redundancy: 3.4 % / Net I/σ(I): 26.2

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACT3.2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G4M

1g4m


Resolution: 2.4→37.03 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 765 4.78 %
Rwork0.197 --
obs0.199 15997 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.18 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 90 44 2807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092822
X-RAY DIFFRACTIONf_angle_d1.2853841
X-RAY DIFFRACTIONf_dihedral_angle_d12.9471731
X-RAY DIFFRACTIONf_chiral_restr0.061434
X-RAY DIFFRACTIONf_plane_restr0.007479
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4001-2.58530.34891440.29233079X-RAY DIFFRACTION99
2.5853-2.84540.3131840.26593037X-RAY DIFFRACTION99
2.8454-3.25690.26221420.21973052X-RAY DIFFRACTION97
3.2569-4.10260.22561630.19212946X-RAY DIFFRACTION95
4.1026-37.03870.21781320.16443118X-RAY DIFFRACTION97

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