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- PDB-4l9i: Bovine G Protein Coupled Receptor Kinase 1 in Complex with Paroxetine -

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Basic information

Entry
Database: PDB / ID: 4l9i
TitleBovine G Protein Coupled Receptor Kinase 1 in Complex with Paroxetine
ComponentsRhodopsin kinase
KeywordsTransferase / membrane protein/inhibitor / AGC family kinase / SER/THR KINASE / RGS HOMOLOGY DOMAIN / G PROTEIN COUPLED RECEPTOR KINASE / GRK / GRK1 / RHODOPSIN KINASE / SSRI / HYDROLYASE / GPCR / PHOSPHORYLATION / membrane protein-inhibitor complex
Function / homology
Function and homology information


rhodopsin kinase / rhodopsin kinase activity / regulation of opsin-mediated signaling pathway / Inactivation, recovery and regulation of the phototransduction cascade / regulation of signal transduction / visual perception / photoreceptor disc membrane / protein autophosphorylation / signal transduction / ATP binding / cytoplasm
Similarity search - Function
Rhodopsin kinase, catalytic domain / GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily ...Rhodopsin kinase, catalytic domain / GPCR kinase / Regulator of G-protein Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Paroxetine / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsHoman, K.T. / Tesmer, J.J.G.
CitationJournal: Mol.Pharmacol. / Year: 2014
Title: Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog.
Authors: Homan, K.T. / Wu, E. / Wilson, M.W. / Singh, P. / Larsen, S.D. / Tesmer, J.J.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rhodopsin kinase
B: Rhodopsin kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,6367
Polymers114,7112
Non-polymers9255
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-34 kcal/mol
Surface area48260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.788, 122.089, 152.892
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 Rhodopsin kinase / / RK / G protein-coupled receptor kinase 1


Mass: 57355.559 Da / Num. of mol.: 2 / Fragment: unp residues 30-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Plasmid: PFastBacDual / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase
#2: Chemical ChemComp-8PR / Paroxetine / (3S,4R)-3-[(1,3-benzodioxol-5-yloxy)methyl]-4-(4-fluorophenyl)piperidine / Paroxetine


Mass: 329.365 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20FNO3 / Comment: antidepressant, inhibitor*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: 12% PEG3350, 1M NaCl, pH 5.75, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1.0793 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0793 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. all: 54845 / Num. obs: 54845 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.32-2.369.20.9491100
2.36-2.49.20.8071100
2.4-2.459.20.7321100
2.45-2.59.20.641100
2.5-2.559.20.5291100
2.55-2.619.20.4561100
2.61-2.689.20.4081100
2.68-2.759.20.3241100
2.75-2.839.20.2721100
2.83-2.929.10.2211100
2.92-3.039.20.1961100
3.03-3.159.20.1571100
3.15-3.299.20.1211100
3.29-3.479.20.0921100
3.47-3.689.10.0751100
3.68-3.979.10.0691100
3.97-4.379.10.0671100
4.37-590.0531100
5-6.298.90.0511100
6.29-508.40.0381100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C4Z

3c4z


Resolution: 2.32→29.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 15.197 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.301 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23053 2774 5.1 %RANDOM
Rwork0.18604 ---
obs0.18833 51966 99.92 %-
all-54845 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.301 Å
Refinement stepCycle: LAST / Resolution: 2.32→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7999 0 62 409 8470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198267
X-RAY DIFFRACTIONr_bond_other_d0.0010.027897
X-RAY DIFFRACTIONr_angle_refined_deg1.3771.97611157
X-RAY DIFFRACTIONr_angle_other_deg0.764318170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6485996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85323.531405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.276151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6911566
X-RAY DIFFRACTIONr_chiral_restr0.0740.21167
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021983
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0822.2613990
X-RAY DIFFRACTIONr_mcbond_other1.0822.2613989
X-RAY DIFFRACTIONr_mcangle_it1.7653.3884984
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3242.4124277
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.322→2.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 191 -
Rwork0.246 3779 -
obs--99.75 %
Refinement TLS params.

Method: refined / 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)
15.90220.47641.38050.99040.02520.9329-0.0243-0.20640.03480.1314-0.0155-0.13090.0787-0.07250.03980.0947-0.00480.0450.092-0.02460.0853-32.5909-12.850414.786
22.4308-0.65520.22453.41880.67990.9346-0.0945-0.0297-0.27610.63850.1174-0.35640.38730.2198-0.02290.34810.0341-0.0520.1764-0.00590.202-12.4574-38.577420.1816
31.7902-0.4414-0.56873.4422-0.43692.62070.1847-0.2045-0.20570.50060.00130.4273-0.0097-0.1473-0.18590.1318-0.06850.00220.12760.05790.1477-34.7137-49.514215.8774
41.77350.00791.73332.53120.28093.61-0.1348-0.06470.02390.18640.034-0.1354-0.0450.03520.10080.08-0.00020.02830.0970.04320.1618-14.682410.746425.0691
53.02120.4780.69223.0493-1.66163.62130.04520.32750.2628-0.24860.06260.4336-0.3966-0.1918-0.10780.20840.0458-0.06980.18190.01750.2361-28.893634.33288.887
62.25890.43490.61725.8177-0.75682.6781-0.1473-0.01030.05470.56160.0641-0.1606-0.1636-0.00580.08330.15850.038-0.080.1251-0.02070.0459-15.506247.431326.4296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 180
2X-RAY DIFFRACTION1A512 - 533
3X-RAY DIFFRACTION1A602
4X-RAY DIFFRACTION1B602
5X-RAY DIFFRACTION1A701 - 807
6X-RAY DIFFRACTION1B701 - 705
7X-RAY DIFFRACTION2A181 - 268
8X-RAY DIFFRACTION2A478 - 511
9X-RAY DIFFRACTION2A601
10X-RAY DIFFRACTION2A894 - 933
11X-RAY DIFFRACTION3A269 - 477
12X-RAY DIFFRACTION3A808 - 893
13X-RAY DIFFRACTION4B31 - 180
14X-RAY DIFFRACTION4B512 - 533
15X-RAY DIFFRACTION4B603
16X-RAY DIFFRACTION4A934 - 935
17X-RAY DIFFRACTION4B706 - 778
18X-RAY DIFFRACTION5B181 - 268
19X-RAY DIFFRACTION5B489 - 511
20X-RAY DIFFRACTION5B601
21X-RAY DIFFRACTION5B779 - 808
22X-RAY DIFFRACTION6B269 - 478
23X-RAY DIFFRACTION6B809 - 874

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