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- PDB-5wg3: Human GRK2 in complex with Gbetagamma subunits and CCG258748 -

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Basic information

Entry
Database: PDB / ID: 5wg3
TitleHuman GRK2 in complex with Gbetagamma subunits and CCG258748
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • Beta-adrenergic receptor kinase 1
KeywordsTransferase/Signaling Protein / 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 / 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 / desensitization of G protein-coupled receptor signaling pathway / 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 / 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 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / Calmodulin induced events / 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 / cardiac muscle contraction / viral genome replication / G protein-coupled receptor binding / receptor internalization / cilium / 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 / Cargo recognition for clathrin-mediated endocytosis / signaling receptor complex adaptor activity / heart development / presynapse / peptidyl-serine phosphorylation / G alpha (s) signalling events / G alpha (q) signalling events / postsynapse / protein kinase activity / symbiont entry into host cell / G protein-coupled receptor signaling pathway / GTPase activity / 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 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 / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / 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 / Roll / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / WD40/YVTN repeat-like-containing domain superfamily / 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-AFM / 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 / MOLECULAR REPLACEMENT / Resolution: 2.896 Å
AuthorsBouley, R. / Tesmer, J.J.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
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 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 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)125,4275
Polymers124,9553
Non-polymers4732
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-46 kcal/mol
Surface area47630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.267, 241.569, 214.813
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: Spodoptera aff. frugiperda 2 RZ-2014 (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 (cattle) / Gene: GNB1
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (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 (cattle) / Gene: GNG2
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (butterflies/moths)
References: UniProt: P63212

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Non-polymers , 3 types, 48 molecules

#4: Chemical ChemComp-AFM / 2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(1H-pyrazol-3-yl)methyl]benzamide


Mass: 448.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25FN6O2
#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.: 46 / 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: 3.16 Å3/Da / Density % sol: 61.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM MES pH 6, 1.1 M NaCl, 8% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.896→50 Å / Num. obs: 35941 / % possible obs: 99 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.1315 / Net I/σ(I): 9.35
Reflection shellResolution: 2.896→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.8547 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3411 / % possible all: 97

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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: 2.896→49.071 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2483 1755 4.89 %
Rwork0.1983 --
obs0.2009 35856 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.896→49.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8104 0 34 46 8184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038304
X-RAY DIFFRACTIONf_angle_d0.55611193
X-RAY DIFFRACTIONf_dihedral_angle_d14.943116
X-RAY DIFFRACTIONf_chiral_restr0.0411208
X-RAY DIFFRACTIONf_plane_restr0.0041450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8955-2.97380.36491390.3262442X-RAY DIFFRACTION95
2.9738-3.06130.38221320.31752613X-RAY DIFFRACTION100
3.0613-3.16010.35561410.30332567X-RAY DIFFRACTION100
3.1601-3.2730.32271220.2672611X-RAY DIFFRACTION100
3.273-3.40410.35391270.25412631X-RAY DIFFRACTION100
3.4041-3.55890.33081290.24612612X-RAY DIFFRACTION100
3.5589-3.74650.26791160.21992619X-RAY DIFFRACTION100
3.7465-3.98110.26671370.19532632X-RAY DIFFRACTION100
3.9811-4.28840.25521340.18282636X-RAY DIFFRACTION100
4.2884-4.71960.18471410.14962655X-RAY DIFFRACTION100
4.7196-5.40180.211470.14982651X-RAY DIFFRACTION100
5.4018-6.80280.21361440.18652686X-RAY DIFFRACTION100
6.8028-49.07850.19941460.16772746X-RAY DIFFRACTION98
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)
14.3608-2.0846-3.14224.06072.76865.9257-0.2786-0.3504-0.5198-0.0077-0.29190.6750.5808-0.42590.50190.97650.05330.23160.49430.04311.076-45.11323.621632.7015
29.14110.9119-0.11813.7621.81686.226-0.41180.1705-0.08-1.42420.3108-0.72210.25471.231-0.00961.16250.18750.28670.4750.05170.8163-18.140318.246415.6434
35.8656-0.2960.52867.1586-0.63056.00060.1182-0.58430.73990.20720.1346-0.889-0.74511.2455-0.24850.6715-0.07970.09980.6243-0.21840.789-21.963136.192233.2227
42.5059-1.05910.46477.6393-1.18752.16340.26990.6234-0.0758-0.8128-0.2304-0.4311-0.51450.20660.00541.48390.13790.29710.40240.02560.9847-22.0669-21.806316.166
51.6048-1.37990.32033.7018-0.65481.64760.13120.1107-0.2335-0.5115-0.00650.29830.067-0.0315-0.11740.96130.00780.12730.3238-0.00810.7963-25.0253-56.088926.9833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:544 OR RESID 803:823 ) )A30 - 184
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:544 OR RESID 803:823 ) )A513 - 544
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 30:184 OR RESID 513:544 OR RESID 803:823 ) )A803 - 823
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 802:802 ) )A185 - 274
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 802:802 ) )A476 - 512
6X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 802:802 ) )A701
7X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 802:802 ) )A802
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 275:474 OR RESID 824:826 ) )A275 - 474
9X-RAY DIFFRACTION3( CHAIN A AND ( RESID 275:474 OR RESID 824:826 ) )A824 - 826
10X-RAY DIFFRACTION4( CHAIN A AND ( RESID 551:668 OR RESID 801:801 ) ) OR ( CHAIN B AND RESID 401:403 )A551 - 668
11X-RAY DIFFRACTION4( CHAIN A AND ( RESID 551:668 OR RESID 801:801 ) ) OR ( CHAIN B AND RESID 401:403 )A801
12X-RAY DIFFRACTION4( CHAIN A AND ( RESID 551:668 OR RESID 801:801 ) ) OR ( CHAIN B AND RESID 401:403 )B401 - 403
13X-RAY DIFFRACTION5( CHAIN B AND ( RESID 2:340 OR RESID 404:414 ) ) OR ( CHAIN G AND ( RESID 7:63 OR RESID 101:106 ) )B2 - 340
14X-RAY DIFFRACTION5( CHAIN B AND ( RESID 2:340 OR RESID 404:414 ) ) OR ( CHAIN G AND ( RESID 7:63 OR RESID 101:106 ) )B404 - 414
15X-RAY DIFFRACTION5( CHAIN B AND ( RESID 2:340 OR RESID 404:414 ) ) OR ( CHAIN G AND ( RESID 7:63 OR RESID 101:106 ) )G7 - 63
16X-RAY DIFFRACTION5( CHAIN B AND ( RESID 2:340 OR RESID 404:414 ) ) OR ( CHAIN G AND ( RESID 7:63 OR RESID 101:106 ) )G101 - 106

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