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- PDB-3psc: Bovine GRK2 in complex with Gbetagamma subunits -

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Basic information

Entry
Database: PDB / ID: 3psc
TitleBovine 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 / Kinase / Serine/threonine-protein kinase / ATP-binding / Membrane / TRANSFERASE-SIGNALING PROTEIN complex
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 / tachykinin receptor signaling pathway ...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 / tachykinin 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 / 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 / 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 / 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 / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Extra-nuclear estrogen signaling / G alpha (z) signalling events / G alpha (s) signalling events / 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 / viral genome replication / cell projection / G protein-coupled receptor binding / intracellular protein transport / 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 / sensory perception of taste / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / presynapse / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / postsynapse / peptidyl-serine phosphorylation / cell population proliferation / protein kinase activity / symbiont entry into host cell / G protein-coupled receptor signaling pathway / protein phosphorylation / GTPase activity / protein-containing complex binding / 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. / 7 Propeller / Methylamine Dehydrogenase; Chain H / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / Few Secondary Structures / Irregular / Helix Hairpins / PH-like domain superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Roll / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / 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
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: 2.67 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 1, 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
Revision 1.3Sep 6, 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 / 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

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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


Theoretical massNumber of molelcules
Total (without water)126,4023
Polymers126,4023
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-49 kcal/mol
Surface area48290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.928, 73.152, 122.780
Angle α, β, γ (deg.)90.00, 115.42, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 59.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG3350, 200 mM NaCl, 100 mM MES pH 6.5, 1 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 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: 2.66→50 Å / Num. obs: 43102 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.073 / Net I/σ(I): 15.7
Reflection shellResolution: 2.67→2.76 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4259 / Rsym value: 0.585 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMW

1omw


Resolution: 2.67→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 31.415 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2165 5 %RANDOM
Rwork0.22278 ---
obs0.22453 40908 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.174 Å2
Baniso -1Baniso -2Baniso -3
1--5.07 Å20 Å2-5.48 Å2
2--7.29 Å20 Å2
3----6.93 Å2
Refinement stepCycle: LAST / Resolution: 2.67→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 0 0 8 8133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228293
X-RAY DIFFRACTIONr_bond_other_d0.0010.025807
X-RAY DIFFRACTIONr_angle_refined_deg1.161.95811171
X-RAY DIFFRACTIONr_angle_other_deg0.813314088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26351008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09823.734399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.332151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561564
X-RAY DIFFRACTIONr_chiral_restr0.0630.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021720
X-RAY DIFFRACTIONr_mcbond_it0.3631.55040
X-RAY DIFFRACTIONr_mcbond_other0.0541.52053
X-RAY DIFFRACTIONr_mcangle_it0.69128104
X-RAY DIFFRACTIONr_scbond_it0.95733253
X-RAY DIFFRACTIONr_scangle_it1.5974.53067
LS refinement shellResolution: 2.665→2.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 154 -
Rwork0.32 2955 -
obs-2955 98.01 %
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)
12.39520.8143-0.54271.5149-1.32646.6646-0.03280.3710.4345-0.0406-0.07470.0099-0.2501-0.33540.10740.35720.0514-0.04590.1911-0.04280.33451.604629.138753.4126
23.4725-0.44970.93952.93890.55195.28570.2974-0.2448-0.81070.4848-0.2494-0.20130.8794-0.1281-0.0480.5638-0.0993-0.26620.1379-0.07610.664545.3575-5.287345.22
36.05571.72982.6884.72752.696911.30670.4157-0.3837-0.37970.3897-0.18210.26481.3247-0.9784-0.23370.4102-0.15980.06190.3233-0.10720.168849.927323.037589.9701
44.06990.07731.98181.63550.57934.0402-0.14560.3510.1844-0.05190.2744-0.2663-0.22911.0685-0.12890.1189-0.10250.08220.3194-0.10520.1667.878343.8367112.149
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 - 340
6X-RAY DIFFRACTION4G8 - 68

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