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- PDB-3pvw: Bovine GRK2 in complex with Gbetagamma subunits and a selective k... -

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Basic information

Entry
Database: PDB / ID: 3pvw
TitleBovine GRK2 in complex with Gbetagamma subunits and a selective kinase inhibitor (CMPD103A)
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/INHIBITOR / Transferase / Serine/threonine-protein kinase / ATP-binding / Inhibitor / Membrane / TRANSFERASE-SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


Calmodulin induced events / Activation of SMO / 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 ...Calmodulin induced events / Activation of SMO / 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 / desensitization of G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of striated muscle contraction / positive regulation of protein localization to cilium / Cargo recognition for clathrin-mediated endocytosis / regulation of the force of heart contraction / G protein-coupled receptor internalization / Activation of the phototransduction cascade / positive regulation of smoothened signaling pathway / 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 / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / regulation of signal transduction / cardiac muscle contraction / 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 / cell projection / intracellular protein transport / signaling receptor complex adaptor activity / presynapse / G protein-coupled receptor binding / peptidyl-threonine phosphorylation / heart development / postsynapse / 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. / GGL domain / 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 signature. / Trp-Asp (WD) repeats circular profile. / 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 / Phosphorylase Kinase; domain 1 / 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 Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-QRX / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsThal, D.M. / Tesmer, J.J.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors.
Authors: Thal, D.M. / Yeow, R.Y. / Schoenau, C. / Huber, J. / Tesmer, J.J.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references

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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: 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)126,8664
Polymers126,4023
Non-polymers4631
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-50 kcal/mol
Surface area48300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.564, 74.227, 123.346
Angle α, β, γ (deg.)90.00, 115.65, 90.00
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 / GRK2 / Beta-ARK-1 / G-protein-coupled receptor kinase 2


Mass: 80578.820 Da / Num. of mol.: 1 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ADRBK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21146, 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 / Fragment: UNP residues 1-68
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-QRX / N-(2,6-difluorobenzyl)-3-({[4-propyl-5-(pyrimidin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide


Mass: 463.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H23F2N7O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 7% PEG3350, 250 mM NaCl, 100 mM MES pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2009
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.49→30 Å / Num. obs: 50352 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.072 / Χ2: 1.385 / Net I/σ(I): 20.45
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRsym value
2.5-2.593.853031.111100
2.59-2.693.853181.10311000.787
2.69-2.823.853131.07111000.568
2.82-2.963.853301.05311000.339
2.96-3.153.852981.10111000.22
3.15-3.393.853511.36711000.141
3.39-3.733.535221.79165.90.109
3.73-4.273.740821.715176.40.058
4.27-5.383.853632.09199.60.043
5.38-303.754721.726199.70.033

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0102phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMW

1omw


Resolution: 2.49→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2741 / WRfactor Rwork: 0.227 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.747 / SU B: 28.961 / SU ML: 0.277 / SU R Cruickshank DPI: 0.4518 / SU Rfree: 0.3053 / Cross valid method: THROUGHOUT / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2849 2550 5.1 %RANDOM
Rwork0.2368 ---
obs0.2393 47727 93.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 205.86 Å2 / Biso mean: 79.0688 Å2 / Biso min: 37.76 Å2
Baniso -1Baniso -2Baniso -3
1--3.91 Å20 Å2-5.4 Å2
2--4.6 Å20 Å2
3----5.36 Å2
Refinement stepCycle: LAST / Resolution: 2.49→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8108 0 34 23 8165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228313
X-RAY DIFFRACTIONr_bond_other_d0.0010.025818
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.96211197
X-RAY DIFFRACTIONr_angle_other_deg0.8073.00114087
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33951006
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92923.719398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.316151510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.521564
X-RAY DIFFRACTIONr_chiral_restr0.0630.21204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021720
X-RAY DIFFRACTIONr_mcbond_it0.3411.55029
X-RAY DIFFRACTIONr_mcbond_other0.0511.52049
X-RAY DIFFRACTIONr_mcangle_it0.65328085
X-RAY DIFFRACTIONr_scbond_it0.91333284
X-RAY DIFFRACTIONr_scangle_it1.4874.53112
LS refinement shellResolution: 2.492→2.557 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 200 -
Rwork0.367 3539 -
all-3739 -
obs--95.58 %
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)
11.97770.6666-0.19241.2075-0.66374.78530.02080.20160.40740.0021-0.02220.0661-0.0288-0.43350.00140.20670.0033-0.00870.1071-0.01240.229851.092529.480253.5554
22.7608-0.4070.32652.17850.25043.69190.228-0.196-0.56660.4113-0.2237-0.1920.5828-0.1185-0.00440.4273-0.131-0.22460.1018-0.00940.491645.2487-5.327345.3517
35.21041.77522.9285.21992.319.94050.3671-0.176-0.27380.4971-0.05020.32021.2461-0.8813-0.31690.3356-0.17930.05250.3966-0.0730.11449.303723.521890.1755
42.8030.13541.62991.51440.5043.6817-0.10960.32060.1059-0.01830.2459-0.2855-0.11620.7523-0.13630.0686-0.08150.06260.241-0.10920.126267.115244.4703112.4536
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 184
2X-RAY DIFFRACTION1A514 - 545
3X-RAY DIFFRACTION2A185 - 513
4X-RAY DIFFRACTION3A546 - 668
5X-RAY DIFFRACTION4B3 - 339
6X-RAY DIFFRACTION4G8 - 68

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