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- PDB-4zrg: Visual arrestin mutant - R175E -

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Basic information

Entry
Database: PDB / ID: 4zrg
TitleVisual arrestin mutant - R175E
ComponentsS-arrestin
KeywordsSIGNALING PROTEIN / arrestin fold / signal termination / GPCR / outer segment
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / response to light stimulus / photoreceptor outer segment / photoreceptor inner segment / G protein-coupled receptor binding / signal transduction / identical protein binding / membrane / cytosol
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
CARBON DIOXIDE / S-arrestin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGranzin, J. / Stadler, A. / Cousin, A. / Schlesinger, R. / Batra-Safferling, R.
CitationJournal: Sci Rep / Year: 2015
Title: Structural evidence for the role of polar core residue Arg175 in arrestin activation.
Authors: Granzin, J. / Stadler, A. / Cousin, A. / Schlesinger, R. / Batra-Safferling, R.
History
DepositionMay 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: S-arrestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3986
Polymers47,1781
Non-polymers2205
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-1 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.373, 72.314, 79.405
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 S-arrestin / 48 kDa protein / Retinal S-antigen / S-AG / Rod photoreceptor arrestin


Mass: 47177.707 Da / Num. of mol.: 1 / Mutation: R175E
Source method: isolated from a genetically manipulated source
Details: N-terminal Tag -7 to 0: WSHPQFEK C-terminal Tag: HHHHHH Pointmutation: R175E
Source: (gene. exp.) Bos taurus (cattle) / Gene: SAG / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P08168
#2: Chemical
ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100mM Tris, 8-18% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97902 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 2.7→41.64 Å / Num. obs: 10993 / % possible obs: 99.92 % / Redundancy: 7.6 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.217 / Net I/σ(I): 10.8
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.924 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UGX

3ugx


Resolution: 2.7→41.637 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 526 4.8 %Random selection
Rwork0.1938 ---
obs0.1961 10957 99.88 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.1 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 15 54 2677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112671
X-RAY DIFFRACTIONf_angle_d1.0063629
X-RAY DIFFRACTIONf_dihedral_angle_d13.463974
X-RAY DIFFRACTIONf_chiral_restr0.072437
X-RAY DIFFRACTIONf_plane_restr0.004458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.97160.32141280.27422550X-RAY DIFFRACTION100
2.9716-3.40150.27471400.2282556X-RAY DIFFRACTION100
3.4015-4.28480.27831250.18372607X-RAY DIFFRACTION100
4.2848-41.640.17471330.15792718X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16031.14370.551.36510.22010.8354-0.0610.0153-0.07570.04310.00270.13370.1874-0.00560.06430.3566-0.0366-0.00660.3740.02310.394219.143825.050224.0152
20.57860.58610.30031.41060.88931.16660.0131-0.1547-0.09020.0251-0.0006-0.060.03020.0009-0.01280.33330.019-0.01160.30260.01280.29392.01-2.00014.895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 179 )
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 360 )

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