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- PDB-3c4y: Crystal Structure of Apo form of G protein coupled receptor kinas... -

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Basic information

Entry
Database: PDB / ID: 3c4y
TitleCrystal Structure of Apo form of G protein coupled receptor kinase 1 at 7.51A
ComponentsRhodopsin kinase
KeywordsTRANSFERASE / Ser/Thr kinase / RGS homology domain / G protein coupled receptor kinase / GRK / GRK1 / rhodopsin kinase / P-loop / autophosphorylation / ATP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Serine/threonine-protein kinase
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 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 ...Rhodopsin kinase, catalytic domain / GPCR kinase / 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. / 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
Similarity search - Domain/homology
Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.509 Å
AuthorsSingh, P. / Tesmer, J.J.G.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structures of rhodopsin kinase in different ligand states reveal key elements involved in G protein-coupled receptor kinase activation.
Authors: Singh, P. / Wang, B. / Maeda, T. / Palczewski, K. / Tesmer, J.J.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhodopsin kinase
B: Rhodopsin kinase


Theoretical massNumber of molelcules
Total (without water)122,8602
Polymers122,8602
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.313, 123.313, 192.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
12A
22B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERTHRTHRAA30 - 26530 - 265
211SERSERTHRTHRBB30 - 26530 - 265
321ALAALAARGARGAA494 - 532494 - 532
421ALAALAARGARGBB494 - 532494 - 532
112ILEILEASPASPAA266 - 472266 - 472
212ILEILEASPASPBB266 - 472266 - 472

NCS ensembles :
ID
1
2

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Components

#1: Protein Rhodopsin kinase / RK / G protein-coupled receptor kinase 1


Mass: 61429.934 Da / Num. of mol.: 2 / Fragment: UNP residues 1-535
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK1, RHOK / Cell line (production host): High 5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase

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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: 3.44 Å3/Da / Density % sol: 64.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 3350, NaCl, MES pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97967 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97967 Å / Relative weight: 1
ReflectionResolution: 7.5→50 Å / Num. obs: 2383

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C4W

3c4w


Resolution: 7.509→20 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 630.819 / SU ML: 2.107 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.18216 --
obs0.18216 2230 99.73 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 194.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 7.509→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7629 0 0 0 7629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227806
X-RAY DIFFRACTIONr_bond_other_d0.0010.025550
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.96910521
X-RAY DIFFRACTIONr_angle_other_deg0.823313406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.45823.513390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.607151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg141564
X-RAY DIFFRACTIONr_chiral_restr0.0550.21106
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028649
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021689
X-RAY DIFFRACTIONr_nbd_refined0.1920.21882
X-RAY DIFFRACTIONr_nbd_other0.1750.25757
X-RAY DIFFRACTIONr_nbtor_refined0.1740.23685
X-RAY DIFFRACTIONr_nbtor_other0.0820.24148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2161
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0180.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.120.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1421.56129
X-RAY DIFFRACTIONr_mcbond_other0.0111.51904
X-RAY DIFFRACTIONr_mcangle_it0.14727498
X-RAY DIFFRACTIONr_scbond_it0.13633748
X-RAY DIFFRACTIONr_scangle_it0.1984.53023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.01 Å

Ens-IDNumberTypeWeight position
13679tight positional0.05
22805tight positional0.05
13679tight thermal0.5
22805tight thermal0.5
LS refinement shellResolution: 7.509→7.676 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.4 156 -
Rfree-0 -
obs--96.3 %
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)
13.3505-3.0015-3.15026.02231.58129.62041.1215-0.1302-0.39460.5679-0.53572.3140.23471.2953-0.5858-0.741-0.7503-0.3619-0.68810.47150.0279-43.656-20.382-21.429
220.5421-6.7006-8.84614.97510.30928.11850.3445-0.4939-0.9998-1.14040.1188-1.51671.39310.0142-0.4633-0.592-0.4799-0.721-0.01731.039-0.4383-21.46-37.546-45.466
33.1476-3.9619-2.393119.755818.48218.02341.4997-1.3468-0.20631.7429-0.6283-0.93441.3649-2.414-0.87140.724-0.6531-0.60630.03820.2363-0.6766-55.612-0.166.917
411.54026.30261.114612.34991.559619.47830.01362.5646-0.1221-0.29181.22691.0589-2.633-1.338-1.24050.26670.1652-0.4181-0.03510.8209-0.6047-28.163-23.496-67.879
516.0951-3.3847-4.11232.0694-2.936711.6951-0.7326-1.9002-1.19751.4265-0.0780.50631.693-2.01730.81061.5805-0.31040.4924-0.00040.66290.3777-70.285-18.30920.825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA30 - 18030 - 180
2X-RAY DIFFRACTION1BB30 - 18030 - 180
3X-RAY DIFFRACTION1AA512 - 532512 - 532
4X-RAY DIFFRACTION1BB512 - 532512 - 532
5X-RAY DIFFRACTION2AA181 - 265181 - 265
6X-RAY DIFFRACTION2AA494 - 511494 - 511
7X-RAY DIFFRACTION3BB181 - 265181 - 265
8X-RAY DIFFRACTION3BB494 - 511494 - 511
9X-RAY DIFFRACTION4AA266 - 474266 - 474
10X-RAY DIFFRACTION5BB266 - 472266 - 472

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