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- PDB-5wg4: Human GRK2 in complex with Gbetagamma subunits and CCG257284 -

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Basic information

Entry
Database: PDB / ID: 5wg4
TitleHuman GRK2 in complex with Gbetagamma subunits and CCG257284
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 / 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 / positive regulation of catecholamine secretion / tachykinin receptor signaling pathway / 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 / positive regulation of catecholamine secretion / 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) / 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 / 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 / Calmodulin induced 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 / G protein-coupled acetylcholine receptor signaling pathway / cilium / receptor internalization / 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 / Cargo recognition for clathrin-mediated endocytosis / presynapse / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (s) signalling events / G alpha (q) signalling events / postsynapse / peptidyl-serine phosphorylation / cell population proliferation / protein kinase activity / symbiont entry into host cell / G protein-coupled receptor signaling pathway / 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 / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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
Chem-AFV / 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: 2.31 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

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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)125,4144
Polymers124,9553
Non-polymers4601
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-48 kcal/mol
Surface area46410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.146, 241.443, 214.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: GRK2, ADRBK1, BARK, BARK1 / Production host: Trichoplusia (butterflies/moths)
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: 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 (cattle) / Gene: GNG2 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: P63212
#4: Chemical ChemComp-AFV / 2-fluoro-5-[(3S,4R)-3-{[(1H-indazol-5-yl)oxy]methyl}piperidin-4-yl]-N-[(pyridin-2-yl)methyl]benzamide


Mass: 459.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FN5O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 50 mM MES pH 6, 6% PEG 3350, 1 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 10, 2016
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.31→47.48 Å / Num. obs: 132268 / % possible obs: 99 % / Redundancy: 2 % / Rsym value: 0.055 / Net I/σ(I): 10.4
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 13.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6936 / Rsym value: 0.928 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNK
Resolution: 2.31→19.956 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2786 3773 2.85 %
Rwork0.2337 --
obs0.235 132207 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.31→19.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8143 0 34 143 8320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028353
X-RAY DIFFRACTIONf_angle_d0.49411260
X-RAY DIFFRACTIONf_dihedral_angle_d13.9045054
X-RAY DIFFRACTIONf_chiral_restr0.041215
X-RAY DIFFRACTIONf_plane_restr0.0031458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.33920.49741420.46254704X-RAY DIFFRACTION96
2.3392-2.36990.43511340.44214629X-RAY DIFFRACTION96
2.3699-2.40240.48461340.43884642X-RAY DIFFRACTION96
2.4024-2.43660.38681430.42964703X-RAY DIFFRACTION96
2.4366-2.47290.46531430.41974600X-RAY DIFFRACTION97
2.4729-2.51150.42351410.40544678X-RAY DIFFRACTION97
2.5115-2.55260.44731380.38974771X-RAY DIFFRACTION97
2.5526-2.59650.36841370.36864716X-RAY DIFFRACTION98
2.5965-2.64360.36771380.36454751X-RAY DIFFRACTION98
2.6436-2.69430.34861420.34944710X-RAY DIFFRACTION98
2.6943-2.74920.36341390.33684758X-RAY DIFFRACTION98
2.7492-2.80880.33681380.33494743X-RAY DIFFRACTION98
2.8088-2.8740.31641340.31824683X-RAY DIFFRACTION97
2.874-2.94560.36121420.3054796X-RAY DIFFRACTION99
2.9456-3.0250.3891370.30364859X-RAY DIFFRACTION100
3.025-3.11370.40711380.28784811X-RAY DIFFRACTION99
3.1137-3.21380.32881440.26564868X-RAY DIFFRACTION100
3.2138-3.32820.30411400.24754771X-RAY DIFFRACTION100
3.3282-3.46080.2751380.24074822X-RAY DIFFRACTION99
3.4608-3.61740.25011420.21084843X-RAY DIFFRACTION100
3.6174-3.80690.24821430.20154785X-RAY DIFFRACTION99
3.8069-4.04350.26221430.19084791X-RAY DIFFRACTION99
4.0435-4.35270.21961430.1674811X-RAY DIFFRACTION99
4.3527-4.78530.19961380.14764849X-RAY DIFFRACTION100
4.7853-5.46530.18281410.15964668X-RAY DIFFRACTION97
5.4653-6.83930.28011430.18614836X-RAY DIFFRACTION100
6.8393-19.95690.18571380.14994836X-RAY DIFFRACTION100
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)
12.6027-0.6592-1.06881.74881.00861.9132-0.2144-0.3444-0.5599-0.2069-0.27230.4950.5664-0.23050.1240.77660.08320.35310.35170.06320.7991-45.17583.230432.3762
26.8071-1.1923-1.9013.77661.67613.5406-0.2183-0.26260.1436-0.81770.2785-0.47920.33150.9493-0.09940.75520.17070.24740.48370.03720.5211-18.573318.401816.0547
33.1698-0.9582-0.71213.5041-0.01373.0807-0.0012-0.67320.553-0.14250.2783-0.6833-0.51561.0698-0.22680.4567-0.09280.13720.6575-0.21130.6212-21.862536.726733.0442
41.3503-0.04630.35163.0748-0.62771.55620.30720.35880.2706-0.5566-0.1688-0.3352-0.41060.05240.01161.22520.16050.37870.32350.0850.8195-22.2145-21.838816.2392
51.3643-0.98160.10523.4172-0.36471.57380.17820.1293-0.1789-0.6275-0.06170.31830.0921-0.0883-0.10720.76830.00320.13440.2521-0.01510.5226-25.0692-55.845227.0003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 31:184 OR RESID 513:547 OR RESID 801:879 ) )A31 - 184
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 31:184 OR RESID 513:547 OR RESID 801:879 ) )A513 - 547
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 31:184 OR RESID 513:547 OR RESID 801:879 ) )A801 - 879
4X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 880:882 ) )A185 - 274
5X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 880:882 ) )A476 - 512
6X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 880:882 ) )A701
7X-RAY DIFFRACTION2( CHAIN A AND ( RESID 185:274 OR RESID 476:512 OR RESID 701:701 OR RESID 880:882 ) )A880 - 882
8X-RAY DIFFRACTION3( CHAIN A AND RESID 275:475 )A275 - 475
9X-RAY DIFFRACTION4( CHAIN A AND ( RESID 548:668 OR RESID 883:883 ) ) OR ( CHAIN B AND ( RESID 401:403 OR RESID 407:448 ) )A548 - 668
10X-RAY DIFFRACTION4( CHAIN A AND ( RESID 548:668 OR RESID 883:883 ) ) OR ( CHAIN B AND ( RESID 401:403 OR RESID 407:448 ) )A883
11X-RAY DIFFRACTION4( CHAIN A AND ( RESID 548:668 OR RESID 883:883 ) ) OR ( CHAIN B AND ( RESID 401:403 OR RESID 407:448 ) )B401 - 403
12X-RAY DIFFRACTION4( CHAIN A AND ( RESID 548:668 OR RESID 883:883 ) ) OR ( CHAIN B AND ( RESID 401:403 OR RESID 407:448 ) )B407 - 448
13X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 6:64 OR RESID 101:106 ) )B2 - 340
14X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 6:64 OR RESID 101:106 ) )G6 - 64
15X-RAY DIFFRACTION5( CHAIN B AND RESID 2:340 ) OR ( CHAIN G AND ( RESID 6:64 OR RESID 101:106 ) )G101 - 106

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