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- PDB-5wg5: Human GRK2 in complex with Gbetagamma subunits and CCG224061 -

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Basic information

Entry
Database: PDB / ID: 5wg5
TitleHuman GRK2 in complex with Gbetagamma subunits and CCG224061
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • Beta-adrenergic receptor kinase 1
KeywordsTRANSFERASE / 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
Function / homology
Function and homology information


negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / 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 the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / 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) / positive regulation of catecholamine secretion / Activation of SMO / 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 / Calmodulin induced events / 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 / cardiac muscle contraction / viral genome replication / G protein-coupled receptor binding / receptor internalization / G protein-coupled acetylcholine receptor signaling pathway / photoreceptor disc membrane / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / Cargo recognition for clathrin-mediated endocytosis / 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 / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / cell population proliferation / protein kinase activity / postsynapse / cilium / 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 / Trp-Asp (WD) repeats signature. / Phosphorylase Kinase; domain 1 / 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 / WD40-repeat-containing domain superfamily / Protein kinase domain / 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
Chem-ZSO / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsBouley, R. / Tesmer, J.J.G.
CitationJournal: Mol. Pharmacol. / Year: 2017
Title: Structural Determinants Influencing the Potency and Selectivity of Indazole-Paroxetine Hybrid G Protein-Coupled Receptor Kinase 2 Inhibitors.
Authors: Bouley, R. / Waldschmidt, H.V. / Cato, M.C. / Cannavo, A. / Song, J. / Cheung, J.Y. / Yao, X.Q. / Koch, W.J. / Larsen, S.D. / Tesmer, J.J.G.
History
DepositionJul 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)125,3045
Polymers124,9553
Non-polymers3502
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-47 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.022, 240.130, 211.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-adrenergic receptor kinase 1 / 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: GRK2, ADRBK1, BARK, BARK1 / Production host: Trichoplusia (butterflies/moths)
References: UniProt: P25098, beta-adrenergic-receptor kinase

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules BG

#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 (domestic cattle) / Gene: GNB1 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: P62871
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7845.078 Da / Num. of mol.: 1 / Mutation: C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: P63212

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Non-polymers , 3 types, 10 molecules

#4: Chemical ChemComp-ZSO / 5-{[(3S,4R)-4-(4-fluorophenyl)piperidin-3-yl]methoxy}-2H-indazole


Mass: 325.380 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H20FN3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / 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: 3.08 Å3/Da / Density % sol: 60.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM MES pH 6, 8-15% PEG3350, 0.8-1.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 28709 / % possible obs: 98 % / Redundancy: 3.9 % / Rsym value: 0.075 / Net I/σ(I): 20.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNK

4pnk


Resolution: 3.1→39.98 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.02
RfactorNum. reflection% reflection
Rfree0.2323 1352 4.79 %
Rwork0.1877 --
obs0.1898 28249 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.1→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 25 8 8183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028358
X-RAY DIFFRACTIONf_angle_d0.45211265
X-RAY DIFFRACTIONf_dihedral_angle_d11.015055
X-RAY DIFFRACTIONf_chiral_restr0.0391214
X-RAY DIFFRACTIONf_plane_restr0.0031458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.21080.33991430.29892642X-RAY DIFFRACTION98
3.2108-3.33930.33131420.27182638X-RAY DIFFRACTION99
3.3393-3.49120.27621290.24162641X-RAY DIFFRACTION98
3.4912-3.67510.27541110.22712700X-RAY DIFFRACTION98
3.6751-3.90520.28261420.19772643X-RAY DIFFRACTION98
3.9052-4.20640.22641210.17352688X-RAY DIFFRACTION98
4.2064-4.62920.20941490.15442706X-RAY DIFFRACTION99
4.6292-5.29770.19791490.14512680X-RAY DIFFRACTION98
5.2977-6.66950.20131400.19072741X-RAY DIFFRACTION98
6.6695-39.98350.19561260.16682818X-RAY DIFFRACTION96
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)
14.9184-0.6325-2.25292.54590.98284.9542-0.2191-0.664-0.18730.55620.02960.91350.3635-0.38580.28350.79880.07070.31830.65540.05610.8185-44.11342.297431.3633
27.4932-0.8445-0.55557.64590.77787.4037-0.17540.0180.4073-0.53970.3609-0.81830.12850.847-0.19280.56350.03610.13780.4704-0.08090.4898-19.561718.247916.5294
33.4731-0.5893-0.29472.64210.45943.1758-0.0267-0.76790.87780.06170.6632-1.0916-0.42271.1872-0.46210.7110.03960.0030.9146-0.45631.0658-21.145135.908533.5803
44.12250.8819-0.2556.1618-3.57547.09620.16790.47990.2002-0.66130.0499-0.3319-0.26950.2449-0.21590.78930.08030.22150.4066-0.06950.5371-21.08-22.00415.7575
51.8703-1.52810.2884.7857-0.77392.29530.12570.1269-0.3174-0.51820.02230.52080.17590.0451-0.1380.59560.0050.07060.4344-0.03590.5137-24.5-56.084626.0784
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:547 OR RESID 801:801 ) )A30 - 184
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:547 OR RESID 801:801 ) )A513 - 547
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:547 OR RESID 801:801 ) )A801
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 477:512 OR RESID 701:701 ) )A185 - 274
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 477:512 OR RESID 701:701 ) )A477 - 512
6X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 477:512 OR RESID 701:701 ) )A701
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 275:473 OR RESID 702:702 ) )A275 - 473
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 275:473 OR RESID 702:702 ) )A702
9X-RAY DIFFRACTION4( CHAIN A AND ( RESID 552:668 OR RESID 802:803 ) )A552 - 668
10X-RAY DIFFRACTION4( CHAIN A AND ( RESID 552:668 OR RESID 802:803 ) )A802 - 803
11X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 7:68 OR RESID 101:105 ) )B2 - 340
12X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 7:68 OR RESID 101:105 ) )G7 - 68
13X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 7:68 OR RESID 101:105 ) )G101 - 105

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