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- PDB-3c4x: Crystal Structure of G protein coupled receptor kinase 1 bound to... -

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Basic information

Entry
Database: PDB / ID: 3c4x
TitleCrystal Structure of G protein coupled receptor kinase 1 bound to ATP and magnesium chloride at 2.9A
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 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'-TRIPHOSPHATE / Rhodopsin kinase GRK1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 ...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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.end_auth_comp_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)123,9948
Polymers122,8602
Non-polymers1,1346
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.116, 95.122, 234.823
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
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRAA31 - 13031 - 130
21ARGARGTHRTHRBB31 - 13031 - 130
32VALVALMETMETAA150 - 464150 - 464
42VALVALMETMETBB150 - 464150 - 464
53THRTHRPROPROAA500 - 533500 - 533
63THRTHRPROPROBB500 - 533500 - 533

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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 (domestic cattle) / Cell line: High 5 / Gene: GRK1, RHOK / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P28327, rhodopsin kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: PEG 3350, NaCl, glycerol, sodium citrate pH 4.3, ATP, magnesium chloride, 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 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97967 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 26629

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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: 2.9→19.75 Å / Cor.coef. Fo:Fc: 0.935 / SU B: 22.335 / SU ML: 0.203 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.19307 --
obs0.19307 26552 96.01 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.257 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7811 0 66 60 7937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228098
X-RAY DIFFRACTIONr_bond_other_d0.0010.025716
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.97710943
X-RAY DIFFRACTIONr_angle_other_deg0.837313821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4045972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99723.575400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.492151405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1481564
X-RAY DIFFRACTIONr_chiral_restr0.0650.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028986
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021746
X-RAY DIFFRACTIONr_nbd_refined0.2230.21678
X-RAY DIFFRACTIONr_nbd_other0.1780.25527
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23879
X-RAY DIFFRACTIONr_nbtor_other0.0850.24321
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.99926347
X-RAY DIFFRACTIONr_mcbond_other0.13421969
X-RAY DIFFRACTIONr_mcangle_it1.24847749
X-RAY DIFFRACTIONr_scbond_it2.3763882
X-RAY DIFFRACTIONr_scangle_it3.28983194
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 / Ens-ID: 1 / Number: 6273 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.440.5
medium thermal0.472
LS refinement shellResolution: 2.901→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.28 1822 -
Rfree-0 -
obs--91.97 %
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)
10.94020.01250.17031.8043-0.11891.08680.0415-0.01430.12660.1166-0.10690.0392-0.2069-0.01220.0654-0.3161-0.01220.0281-0.26530.065-0.2363-41.4033-3.426.5411
20.77650.12061.00460.44770.26922.0103-0.1081-0.14110.2540.04390.06570.079-0.0061-0.00940.04240.0778-0.006-0.08130.0731-0.07010.032-7.5783-4.010163.4084
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA30 - 53330 - 533
2X-RAY DIFFRACTION2BB31 - 53331 - 533

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