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Entry
Database: PDB / ID: 1omw
TitleCrystal Structure of the complex between G Protein-Coupled Receptor Kinase 2 and Heterotrimeric G Protein beta 1 and gamma 2 subunits
Components
  • G-protein coupled receptor kinase 2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 1
KeywordsTRANSFERASE / WD-40 repeat
Function / homology
Function and homology information


Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / Edg-2 lysophosphatidic acid receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway ...Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / Edg-2 lysophosphatidic acid receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / negative regulation of striated muscle contraction / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Cargo recognition for clathrin-mediated endocytosis / positive regulation of protein localization to cilium / desensitization of G protein-coupled receptor signaling pathway / cytoplasmic side of mitochondrial outer membrane / regulation of the force of heart contraction / Activation of the phototransduction cascade / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of signal transduction / cardiac muscle contraction / adenylate cyclase-activating adrenergic receptor signaling pathway / viral genome replication / cell projection / intracellular protein transport / G protein-coupled receptor binding / G protein-coupled acetylcholine receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / sensory perception of taste / presynapse / signaling receptor complex adaptor activity / heart development / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / protein phosphorylation / protein kinase activity / postsynapse / G protein-coupled receptor signaling pathway / GTPase activity / synapse / symbiont entry into host cell / protein-containing complex binding / ATP binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1270 / GPCR kinase / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / 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 ...Helix Hairpins - #1270 / GPCR kinase / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / Pleckstrin homology domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Few Secondary Structures / Irregular / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Helix Hairpins / PH-like domain superfamily / WD domain, G-beta repeat / Roll / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Phosphorylase Kinase; domain 1 / Trp-Asp (WD) repeats signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Trp-Asp (WD) repeats profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta-adrenergic receptor kinase 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLodowski, D.T. / Pitcher, J.A. / Capel, W.D. / Lefkowitz, R.J. / Tesmer, J.J.G.
CitationJournal: Science / Year: 2003
Title: Keeping G proteins at Bay: A Complex Between G Protein-Coupled Receptor Kinase 2 and G-Beta-Gamma
Authors: Lodowski, D.T. / Pitcher, J.A. / Capel, W.D. / Lefkowitz, R.J. / Tesmer, J.J.G.
History
DepositionFeb 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Advisory / Refinement description
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: G-protein coupled receptor kinase 2
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit


Theoretical massNumber of molelcules
Total (without water)125,5743
Polymers125,5743
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.200, 72.500, 122.790
Angle α, β, γ (deg.)90.00, 115.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein G-protein coupled receptor kinase 2 / GRK2 / Beta-ARK-1 / Beta-adrenergic receptor kinase 1


Mass: 79749.922 Da / Num. of mol.: 1 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GRK2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P21146, EC: 2.7.1.126
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 1 / Transducin beta chain 1


Mass: 37416.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma-2 subunit / G gamma-I


Mass: 8406.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P63212
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.75
Details: PEG 3350, Sodium Chloride, CHAPS, ATP, Magnesium Chloride, Mastoparan , MES pH 5.75, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Lodowski, D.T., (2003) Acta Crystallogr., D59, 936.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
2100 mMMES1reservoirpH5.25
3200 mM1reservoirNaCl
41 mMinositol-3,4,5-triphosphate1reservoir
55 mM1reservoirMgCl2
66.9-7.8 %PEG33501reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU200H11.5418
SYNCHROTRONALS 8.2.121
Detector
TypeIDDetectorDateDetails
MARRESEARCH1IMAGE PLATEJun 15, 2002Osmic confocal Max-flux
ADSC QUANTUM 2102CCDJul 17, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1double crystal si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
211
ReflectionResolution: 2.5→20 Å / Num. all: 135084 / Num. obs: 56160 / % possible obs: 73.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 2.4 % / Biso Wilson estimate: 37.42 Å2 / Rsym value: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 0.67 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1977 / Rsym value: 0.253 / % possible all: 12.7
Reflection
*PLUS
Num. obs: 38258 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 12.7 % / Rmerge(I) obs: 0.253

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ABG, 1ATP, 1BAK, 1DK8

1abg

1atp

1bak

1dk8


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.95 / SU B: 10.266 / SU ML: 0.205 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement
Cross valid method: The structure was initally solved with R-free as the cross validation method, but for the last three rounds of refinement, the structure was refined against all of the data.
σ(F): -2 / ESU R: 0.72 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the extreme anisotropy of the data, a three dimensional ellipsoid with resolution limits corresponding to the maximum diffraction in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Due to the extreme anisotropy of the data, a three dimensional ellipsoid with resolution limits corresponding to the maximum diffraction in each direction was defined to select reflections used in refinement. These diffraction limits were 2.4, 2.8, 3.0 Angstroms. The 2.4 A direction corresponds to 37.9 degrees inclined from the a* axis, the 2.8 A direction corresponds to the b* axis and the 3.0 A direction corresponds to direction 1 X b*.
RfactorNum. reflection% reflectionSelection details
Rfree0.25196 1942 -RANDOM
Rwork0.20223 ---
all0.2164 38249 --
obs0.21648 36307 73.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.933 Å2
Baniso -1Baniso -2Baniso -3
1--6.04 Å20 Å2-6.28 Å2
2--8.91 Å20 Å2
3----8.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 0 0 26 8151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0218293
X-RAY DIFFRACTIONr_bond_other_d0.0020.027481
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.95311173
X-RAY DIFFRACTIONr_angle_other_deg1.007317440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16951009
X-RAY DIFFRACTIONr_chiral_restr0.1030.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029184
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021721
X-RAY DIFFRACTIONr_nbd_refined0.2320.21755
X-RAY DIFFRACTIONr_nbd_other0.2440.28637
X-RAY DIFFRACTIONr_nbtor_other0.0990.24925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2370.22
X-RAY DIFFRACTIONr_mcbond_it0.8941.55040
X-RAY DIFFRACTIONr_mcangle_it1.69128106
X-RAY DIFFRACTIONr_scbond_it2.52933253
X-RAY DIFFRACTIONr_scangle_it4.1244.53067
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 0 -
Rwork0.279 413 -
obs-413 12.7 %
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)
12.69170.4234-0.1071.889-0.62575.6291-0.06480.23540.507-0.1081-0.14240.0748-0.4646-0.36710.20720.38240.0989-0.0830.2688-0.10490.375451.150228.656754.375
24.1555-0.3907-3.06344.4397-0.86083.41810.2219-0.9069-0.71660.6056-0.37330.14531.2866-0.61560.15141.1043-0.4606-0.33550.8835-0.08530.69538.2759-0.937358.4661
33.3344-0.10310.80442.2885-0.58933.04590.35320.2696-0.90170.0999-0.1625-0.33160.88840.4532-0.19070.73270.0432-0.27940.4412-0.28880.886448.4148-7.290339.6204
47.0490.8293.99134.35692.607911.15390.4849-0.3111-0.56480.4657-0.31110.1321.4654-0.8157-0.17380.5061-0.14290.06680.2863-0.16070.186150.965621.903190.3772
53.7999-0.08371.65581.70830.47513.4441-0.11640.40620.2298-0.05040.2495-0.1703-0.16411.2226-0.13310.1601-0.13620.110.1297-0.13930.243868.540543.3997112.2574
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 187
2X-RAY DIFFRACTION1A512 - 550
3X-RAY DIFFRACTION1A690
4X-RAY DIFFRACTION1A691
5X-RAY DIFFRACTION1A694
6X-RAY DIFFRACTION1A703
7X-RAY DIFFRACTION2A188 - 274
8X-RAY DIFFRACTION2A692
9X-RAY DIFFRACTION2A701
10X-RAY DIFFRACTION3A275 - 475
11X-RAY DIFFRACTION3A496 - 511
12X-RAY DIFFRACTION3A695
13X-RAY DIFFRACTION3A696 - 697
14X-RAY DIFFRACTION3A698
15X-RAY DIFFRACTION4A551 - 569
16X-RAY DIFFRACTION4A576 - 668
17X-RAY DIFFRACTION4A693
18X-RAY DIFFRACTION5B2 - 340
19X-RAY DIFFRACTION5G8 - 68
20X-RAY DIFFRACTION5B341 - 342
21X-RAY DIFFRACTION5B343 - 344
22X-RAY DIFFRACTION5B345
23X-RAY DIFFRACTION5B346 - 347
24X-RAY DIFFRACTION5B348
25X-RAY DIFFRACTION5B349 - 350
26X-RAY DIFFRACTION5G69
27X-RAY DIFFRACTION5G70
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.024
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.035

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