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- PDB-3cik: Human GRK2 in Complex with Gbetagamma subunits -

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Basic information

Entry
Database: PDB / ID: 3cik
TitleHuman GRK2 in Complex with Gbetagamma subunits
Components
  • Beta-adrenergic receptor kinase 1G protein-coupled receptor kinase 2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
  • Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
KeywordsTransferase/Signaling protein / protein kinase / complex / G protein / receptor / WD40 repeat / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transducer / WD repeat / Lipoprotein / Membrane / Phosphoprotein / Prenylation / Transferase-Signaling protein COMPLEX
Function / homology
Function and homology information


beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway / positive regulation of catecholamine secretion / Olfactory Signaling Pathway ...beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / tachykinin receptor signaling pathway / positive regulation of catecholamine secretion / Olfactory Signaling Pathway / desensitization of G protein-coupled receptor signaling pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Activation of SMO / negative regulation of striated muscle contraction / regulation of the force of heart contraction / Activation of the phototransduction cascade / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / Adrenaline,noradrenaline inhibits insulin secretion / 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 / Glucagon-type ligand receptors / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (q) signalling events / Calmodulin induced events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / cardiac muscle contraction / regulation of signal transduction / G protein-coupled acetylcholine receptor signaling pathway / viral genome replication / 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 / cilium / signaling receptor complex adaptor activity / receptor internalization / presynapse / G protein-coupled receptor binding / Cargo recognition for clathrin-mediated endocytosis / G alpha (s) signalling events / G alpha (q) signalling events / peptidyl-threonine phosphorylation / postsynapse / heart development / G protein-coupled receptor signaling pathway / peptidyl-serine phosphorylation / protein kinase activity / GTPase activity / viral entry into host cell / protein phosphorylation / ATP binding / membrane / plasma membrane / cytosol / cytoplasm
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, subdomain 2 / RGS domain / RGS domain profile. ...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, subdomain 2 / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / YVTN repeat-like/Quinoprotein amine dehydrogenase / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain superfamily / G-protein gamma-like domain / GGL domain / G protein gamma subunit-like motifs / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Few Secondary Structures / Irregular / G-protein beta WD-40 repeat / Helix Hairpins / PH-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / 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 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 speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsTesmer, J.J.G. / Lodowski, D.T.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure of human G protein-coupled receptor kinase 2 in complex with the kinase inhibitor balanol.
Authors: Tesmer, J.J. / Tesmer, V.M. / Lodowski, D.T. / Steinhagen, H. / Huber, J.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,5414
Polymers125,5163
Non-polymers241
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-44.6 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.736, 73.604, 122.914
Angle α, β, γ (deg.)90.000, 115.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 79692.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADRBK1, BARK, BARK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P25098, beta-adrenergic-receptor kinase
#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-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 (cattle) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 8406.658 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 200 mM NaCl, 5% ethylene glycol, 6.3% PEG 3350, pH 5.25, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.033 Å
DetectorDetector: CCD / Date: Feb 23, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 38796 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.101 / Χ2: 1.286 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.850.54538400.635198.8
2.85-2.960.41638540.648199
2.96-3.10.33338780.773199.2
3.1-3.260.23138630.93199.5
3.26-3.460.15638941.049199.5
3.46-3.730.11838891.337199.3
3.73-4.110.09339091.649199.3
4.11-4.70.07338981.971199.5
4.7-5.920.06639551.838199.6
5.92-500.05638162.173194.3

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Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
RefinementResolution: 2.75→25 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 19.966 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.668 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.269 1949 -
Rwork0.208 --
all0.208 38772 -
obs0.208 38772 98.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-2.18 Å2
2--3.35 Å20 Å2
3----4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 1 19 8185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228337
X-RAY DIFFRACTIONr_bond_other_d0.0010.025845
X-RAY DIFFRACTIONr_angle_refined_deg1.311.95711223
X-RAY DIFFRACTIONr_angle_other_deg0.86314168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63851013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01823.663404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.585151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4371567
X-RAY DIFFRACTIONr_chiral_restr0.0730.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021737
X-RAY DIFFRACTIONr_nbd_refined0.2160.21675
X-RAY DIFFRACTIONr_nbd_other0.1850.25871
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23932
X-RAY DIFFRACTIONr_nbtor_other0.0870.24525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.21
X-RAY DIFFRACTIONr_mcbond_it1.17226545
X-RAY DIFFRACTIONr_mcbond_other0.10522064
X-RAY DIFFRACTIONr_mcangle_it1.74358138
X-RAY DIFFRACTIONr_scbond_it2.89553834
X-RAY DIFFRACTIONr_scangle_it4.238103085
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 152 -
Rwork0.311 2780 -
obs-2780 97.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.6168-0.10010.08882.19020.66253.87970.0193-0.1444-0.23250.2395-0.1960.01990.5964-0.00020.1767-0.0782-0.0589-0.1211-0.1472-0.0357-0.064243.261-5.27147.423
22.20150.0010.85561.04480.04012.5809-0.06430.13470.1827-0.06520.0657-0.1747-0.21020.3488-0.0014-0.0991-0.1120.0059-0.0954-0.0482-0.187567.11943.43113.012
32.11480.0637-0.34172.04610.0674.90830.11610.33420.3344-0.1558-0.1158-0.1041-0.47850.0406-0.0003-0.04690.0631-0.0601-0.0869-0.0446-0.130750.88529.33453.618
45.16110.45061.9023.53091.40737.27530.3342-0.4334-0.20440.3678-0.30880.20950.9071-0.8172-0.02540.031-0.14630.0226-0.0208-0.0955-0.314548.77123.42890.601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA185 - 513185 - 513
2X-RAY DIFFRACTION1AD - E690 - 7001 - 10
3X-RAY DIFFRACTION2BB2 - 3402 - 340
4X-RAY DIFFRACTION2GC8 - 6814 - 74
5X-RAY DIFFRACTION2BF341 - 3421 - 2
6X-RAY DIFFRACTION2BF343 - 3473 - 7
7X-RAY DIFFRACTION3AA29 - 18429 - 184
8X-RAY DIFFRACTION3AA514 - 545514 - 545
9X-RAY DIFFRACTION3AE70111
10X-RAY DIFFRACTION4AA546 - 669546 - 669

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