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- PDB-1ym7: G Protein-Coupled Receptor Kinase 2 (GRK2) -

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Basic information

Entry
Database: PDB / ID: 1ym7
TitleG Protein-Coupled Receptor Kinase 2 (GRK2)
ComponentsBeta-adrenergic receptor kinase 1
KeywordsTRANSFERASE / G protein / kinase / GPCR / GRK2 / Beta-ARK1
Function / homology
Function and homology information


Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / negative regulation of striated muscle contraction ...Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / negative regulation of striated muscle contraction / desensitization of G protein-coupled receptor signaling pathway / positive regulation of protein localization to cilium / Cargo recognition for clathrin-mediated endocytosis / regulation of the force of heart contraction / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / G alpha (s) signalling events / G alpha (q) signalling events / regulation of signal transduction / cardiac muscle contraction / cell projection / G protein-coupled receptor binding / intracellular protein transport / G protein-coupled acetylcholine receptor signaling pathway / presynapse / postsynapse / peptidyl-serine phosphorylation / protein kinase activity / G protein-coupled receptor signaling pathway / protein phosphorylation / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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. ...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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / 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
Beta-adrenergic receptor kinase 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å
AuthorsLodowski, D.T. / Barnhill, J.F. / Pyskadlo, R.M. / Ghirlando, R. / Sterne-Marr, R. / Tesmer, J.J.G.
CitationJournal: Biochemistry / Year: 2005
Title: The role of Gbetagamma and domain interfaces in the activation of G protein-coupled receptor kinase 2
Authors: Lodowski, D.T. / Barnhill, J.F. / Pyskadlo, R.M. / Ghirlando, R. / Sterne-Marr, R. / Tesmer, J.J.G.
History
DepositionJan 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-adrenergic receptor kinase 1
B: Beta-adrenergic receptor kinase 1
C: Beta-adrenergic receptor kinase 1
D: Beta-adrenergic receptor kinase 1


Theoretical massNumber of molelcules
Total (without water)319,0004
Polymers319,0004
Non-polymers00
Water00
1
A: Beta-adrenergic receptor kinase 1


Theoretical massNumber of molelcules
Total (without water)79,7501
Polymers79,7501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-adrenergic receptor kinase 1


Theoretical massNumber of molelcules
Total (without water)79,7501
Polymers79,7501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-adrenergic receptor kinase 1


Theoretical massNumber of molelcules
Total (without water)79,7501
Polymers79,7501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-adrenergic receptor kinase 1


Theoretical massNumber of molelcules
Total (without water)79,7501
Polymers79,7501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.162, 82.156, 218.795
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25B
16A
26B
36C
46D

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
111SERSERILEILEAA29 - 18429 - 184
221SERSERILEILEBB29 - 18429 - 184
331SERSERILEILECC29 - 18429 - 184
441SERSERILEILEDD29 - 18429 - 184
152HISHISGLYGLYAA185 - 475185 - 475
262HISHISGLYGLYBB185 - 475185 - 475
372HISHISGLYGLYCC185 - 475185 - 475
482HISHISGLYGLYDD185 - 475185 - 475
193LYSLYSTHRTHRAA494 - 512494 - 512
2103LYSLYSTHRTHRBB494 - 512494 - 512
3113LYSLYSTHRTHRCC494 - 512494 - 512
4123LYSLYSTHRTHRDD494 - 512494 - 512
1134ILEILEGLUGLUAA513 - 537513 - 537
2144ILEILEGLUGLUBB513 - 537513 - 537
3154ILEILEGLUGLUCC513 - 537513 - 537
4164ILEILEGLUGLUDD513 - 537513 - 537
1175ALAALALEULEUAA538 - 555538 - 555
2185ALAALALEULEUBB538 - 555538 - 555
1196GLYGLYGLNGLNAA556 - 656556 - 656
2206GLYGLYGLNGLNBB556 - 656556 - 656
3216GLYGLYGLNGLNCC556 - 656556 - 656
4226GLYGLYGLNGLNDD556 - 656556 - 656

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-adrenergic receptor kinase 1 / Beta-ARK-1 / G- protein coupled receptor kinase 2


Mass: 79749.922 Da / Num. of mol.: 4 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ADRBK1, GRK2 / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21146, EC: 2.7.1.126

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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: 3.2 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: HEPES, phosphoserine, sodium Chloride, Glycerol, PEG 8000, Urea, Dithiothreitol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 25, 2003
RadiationMonochromator: 100 micron collimator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.5→20 Å / Num. all: 24354 / Num. obs: 24246 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.42 % / Rsym value: 0.055 / Net I/σ(I): 21.4
Reflection shellResolution: 4.5→4.66 Å / Redundancy: 3.35 % / Mean I/σ(I) obs: 2.46 / Num. unique all: 2406 / Rsym value: 0.45 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OMW

1omw


Resolution: 4.5→14.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 218.079 / SU ML: 1.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 1.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS WERE ADDED IN THE RIDING POSITIONS. TLS REFINEMENT UTILIZED
RfactorNum. reflection% reflectionSelection details
Rfree0.27868 1197 5 %RANDOM
Rwork0.22358 ---
all0.22638 22730 --
obs0.22638 22700 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å21.9 Å2
2---2.33 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 4.5→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19846 0 0 0 19846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02220365
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.96727358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.32952419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20823.731008
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.176153879
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.85415152
X-RAY DIFFRACTIONr_chiral_restr0.1290.22882
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215328
X-RAY DIFFRACTIONr_nbd_refined0.2940.28477
X-RAY DIFFRACTIONr_nbtor_refined0.3290.212726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2763
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.246
X-RAY DIFFRACTIONr_mcbond_it01.512643
X-RAY DIFFRACTIONr_mcangle_it0219491
X-RAY DIFFRACTIONr_scbond_it038993
X-RAY DIFFRACTIONr_scangle_it04.57867
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1316tight positional0.080.05
12B1316tight positional0.070.05
13C1316tight positional0.080.05
14D1316tight positional0.060.05
21A2321tight positional0.060.05
22B2321tight positional0.070.05
23C2321tight positional0.070.05
24D2321tight positional0.060.05
31A158tight positional0.060.05
32B158tight positional0.060.05
33C158tight positional0.060.05
34D158tight positional0.060.05
41A209tight positional0.070.05
42B209tight positional0.060.05
43C209tight positional0.060.05
44D209tight positional0.060.05
51A149tight positional0.070.05
61A822tight positional0.060.05
62B822tight positional0.050.05
63C822tight positional0.050.05
64D822tight positional0.050.05
11A1316tight thermal00.5
12B1316tight thermal00.5
13C1316tight thermal00.5
14D1316tight thermal00.5
21A2321tight thermal00.5
22B2321tight thermal00.5
23C2321tight thermal00.5
24D2321tight thermal00.5
31A158tight thermal00.5
32B158tight thermal00.5
33C158tight thermal00.5
34D158tight thermal00.5
41A209tight thermal00.5
42B209tight thermal00.5
43C209tight thermal00.5
44D209tight thermal00.5
51A149tight thermal00.5
61A822tight thermal00.5
62B822tight thermal00.5
63C822tight thermal00.5
64D822tight thermal00.5
LS refinement shellResolution: 4.5→4.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.481 70 -
Rwork0.423 1580 -
obs--100 %
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)
16.1018-1.84880.11248.61582.18865.5113-0.25620.1963-0.87060.19360.36080.74180.4945-0.5679-0.1046-0.6921-0.1406-0.5256-0.275-0.1457-0.621783.003-48.02815.527
26.2796-3.1751-1.29459.67810.11386.4703-0.18290.6361.05910.08610.5639-0.1503-0.78260.1669-0.381-1.13420.0653-0.0755-0.65520.2137-0.788731.48216.06615.28
34.7244-1.3973-1.90377.12875.103915.7825-0.4504-0.069-0.23550.4753-0.6787-0.81931.52160.37541.1291-1.11850.0283-0.3167-0.1370.1235-0.5216146.46-73.44476.593
45.54630.54670.09953.9838-3.43987.94260.13051.05740.55-1.4078-0.31980.5988-0.4385-0.39730.18930.3910.12170.2234-0.1758-0.04320.5086-43.42127.55463.683
56.9346-5.81275.0738.3575-4.31346.8616-0.2029-0.37670.07570.36140.2289-0.4877-0.90370.692-0.0261-0.61660.2581-0.5017-0.4556-0.1605-0.699595.036-26.47640.85
611.4313-2.2184-6.63245.39281.46577.66440.2932-0.52530.17490.1658-0.1331.16251.0466-0.3773-0.1603-0.7490.04930.3005-0.89410.1382-0.407218.356-7.61439.092
72.1379-1.20615.49513.3642-1.005615.7591-0.1645-0.11230.51620.2159-0.12020.5037-0.7747-0.81150.2847-0.9010.0609-0.63260.2284-0.1982-0.3213122.606-46.21179.391
87.0425-2.8065-7.86843.80721.75939.4956-0.0205-0.72670.23480.5410.3274-1.0095-0.04390.6048-0.3069-0.7867-0.10610.5008-0.113-0.22890.6977-17.6765.48873.415
910.02971.9493-0.86738.63062.08789.11030.25530.25841.94450.0192-0.31130.8581-2.37070.04810.0560.15640.671-0.4052-0.38880.14860.396468.889-2.48633.925
1010.50912.95483.87256.39153.59693.79620.8580.1825-2.51150.5056-0.3952-1.23362.04430.239-0.46290.31210.9789-0.018-0.30270.27470.523346.644-29.29333.209
1113.58111.0967-2.34186.2166-2.9198.24330.1087-1.50281.17180.91440.47540.6271-1.1859-0.0304-0.58410.23840.0026-0.63820.1827-0.4738-0.3455136.503-38.587111.95
126.89921.192-1.99050.4434-0.53055.37820.4061-1.3891-0.74391.5941-0.181-0.30910.7576-0.1101-0.22510.7830.01350.49530.57410.30420.8032-36.702-6.431101.792
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA185 - 513185 - 513
2X-RAY DIFFRACTION2BB185 - 513185 - 513
3X-RAY DIFFRACTION3CC185 - 513185 - 513
4X-RAY DIFFRACTION4DD185 - 513185 - 513
5X-RAY DIFFRACTION5AA29 - 18429 - 184
6X-RAY DIFFRACTION5AA514 - 538514 - 538
7X-RAY DIFFRACTION6BB29 - 18429 - 184
8X-RAY DIFFRACTION6BB514 - 538514 - 538
9X-RAY DIFFRACTION7CC29 - 18429 - 184
10X-RAY DIFFRACTION7CC514 - 538514 - 538
11X-RAY DIFFRACTION8DD29 - 18429 - 184
12X-RAY DIFFRACTION8DD514 - 538514 - 538
13X-RAY DIFFRACTION9AA539 - 656539 - 656
14X-RAY DIFFRACTION10BB539 - 656539 - 656
15X-RAY DIFFRACTION11CC539 - 656539 - 656
16X-RAY DIFFRACTION12DD539 - 656539 - 656

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