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- PDB-3c50: Crystal Structure of G protein coupled receptor kinase 1 bound to... -

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Basic information

Entry
Database: PDB / ID: 3c50
TitleCrystal Structure of G protein coupled receptor kinase 1 bound to ADP and magnesium chloride at 2.6A
ComponentsRhodopsin kinase
KeywordsTRANSFERASE / Ser/Thr kinase / RGS homology domain / G protein coupled receptor kinase / GRK / GRK1 / rhodopsin kinase / P-loop / autophosphorylation / ADP / 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 Signalling 4, domain 2 / Regulator of G-protein Signalling 4; domain 2 / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / 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 domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
ADENOSINE-5'-DIPHOSPHATE / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 / Refinement description / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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)124,29017
Polymers122,8602
Non-polymers1,43015
Water5,459303
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.504, 122.304, 174.076
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERCYSCYS5AA30 - 4730 - 47
211SERSERCYSCYS5BB30 - 4730 - 47
121PHEPHEPROPRO5AA58 - 53358 - 533
221PHEPHEPROPRO5BB58 - 53358 - 533
112HOHHOHHOHHOH4AR571 - 735
212HOHHOHHOHHOH4BS570 - 707

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#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 (domestic 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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Non-polymers , 5 types, 318 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.84 Å3/Da / Density % sol: 56.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: PEG 8000, NaCl, glycerol, MES pH 6.25, ADP, magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 43786

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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 3C4Z

3c4z


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.946 / SU B: 14.954 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.18984 --
obs0.18984 43677 99.85 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.969 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å20 Å2
2---2.99 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7989 0 78 303 8370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228326
X-RAY DIFFRACTIONr_bond_other_d0.0010.025882
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.97711256
X-RAY DIFFRACTIONr_angle_other_deg0.838314229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.59851005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05123.554408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.064151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2161566
X-RAY DIFFRACTIONr_chiral_restr0.0660.21177
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021796
X-RAY DIFFRACTIONr_nbd_refined0.2150.21657
X-RAY DIFFRACTIONr_nbd_other0.1810.25792
X-RAY DIFFRACTIONr_nbtor_refined0.1840.24022
X-RAY DIFFRACTIONr_nbtor_other0.0840.24311
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2348
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7021.56527
X-RAY DIFFRACTIONr_mcbond_other0.0931.52028
X-RAY DIFFRACTIONr_mcangle_it0.76927993
X-RAY DIFFRACTIONr_scbond_it1.17933963
X-RAY DIFFRACTIONr_scangle_it1.7944.53263
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

Ens-IDNumberTypeRms dev position (Å)Weight position
12864medium positional0.260.5
2107medium positional0.330.5
13952loose positional0.495
12864medium thermal0.562
2107medium thermal1.532
13952loose thermal0.9210
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.268 3124 -
Rfree-0 -
obs--99.94 %
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)
10.5691-0.212-0.10941.84380.19370.50210.04710.09340.0426-0.12-0.0199-0.1561-0.0262-0.042-0.0272-0.05250.01540.0137-0.06760.0181-0.1958-3.70933.816-16.534
20.51390.7702-0.29312.9449-0.46130.7089-0.14220.0502-0.0884-0.17440.0559-0.09960.1091-0.02820.08630.0002-0.0271-0.0194-0.03520.0018-0.09826.743-31.777-21.85
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 533
2X-RAY DIFFRACTION1A571 - 735
3X-RAY DIFFRACTION1A570
4X-RAY DIFFRACTION2B30 - 533
5X-RAY DIFFRACTION2B570 - 707

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