[English] 日本語
Yorodumi
- PDB-5wg4: Human GRK2 in complex with Gbetagamma subunits and CCG257284 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wg4
TitleHuman GRK2 in complex with Gbetagamma subunits and CCG257284
Components
  • Beta-adrenergic receptor kinase 1
  • 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


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 / alpha-2A adrenergic receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / 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 / alpha-2A adrenergic receptor binding / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / 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 / desensitization of G protein-coupled receptor signaling pathway / Activation of SMO / cytoplasmic side of mitochondrial outer membrane / Activation of the phototransduction cascade / regulation of the force of heart contraction / 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 / G-protein beta-subunit binding / cellular response to prostaglandin E stimulus / heterotrimeric G-protein complex / presynapse / sensory perception of taste / 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 / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1270 / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GPCR kinase / 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 / Transducin (heterotrimeric G protein), gamma chain / G Protein Gi Gamma 2 / GPCR kinase / 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 / PH domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / WD40 repeat, conserved site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Trp-Asp (WD) repeats signature. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Protein kinase domain / WD40-repeat-containing domain superfamily / 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-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 (domestic 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#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
#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
#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


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PNK

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

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)
12.6027-0.6592-1.06881.74881.00861.9132-0.2144-0.3444-0.5599-0.2069-0.27230.4950.5664-0.23050.1240.77660.08320.35310.35170.06320.7991-45.17583.230432.3762
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more