[English] 日本語
Yorodumi
- PDB-3cik: Human GRK2 in Complex with Gbetagamma subunits -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cik
TitleHuman 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 / protein kinase / complex / G protein / receptor / WD40 repeat / ATP-binding / Nucleotide-binding / Serine/threonine-protein kinase / Transferase / Transducer / WD repeat / Lipoprotein / Membrane / Phosphoprotein / Prenylation / 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 / desensitization of G protein-coupled receptor 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 / 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 / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (q) signalling events / Calmodulin induced events / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / cardiac muscle contraction / regulation of signal transduction / G protein-coupled acetylcholine receptor signaling pathway / viral genome replication / 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 / cilium / signaling receptor complex adaptor activity / receptor internalization / presynapse / G protein-coupled receptor binding / Cargo recognition for clathrin-mediated endocytosis / G alpha (s) signalling events / G alpha (q) signalling events / peptidyl-threonine phosphorylation / postsynapse / heart development / G protein-coupled receptor signaling pathway / peptidyl-serine phosphorylation / protein kinase activity / GTPase activity / viral entry into host cell / protein phosphorylation / 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. / PH domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein, gamma subunit / G-protein gamma subunit domain profile. / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Few Secondary Structures / Irregular / G-protein beta WD-40 repeat / Helix Hairpins / PH-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain / Phosphorylase Kinase; domain 1 / 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 speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.75 Å
AuthorsTesmer, J.J.G. / Lodowski, D.T.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure of human G protein-coupled receptor kinase 2 in complex with the kinase inhibitor balanol.
Authors: Tesmer, J.J. / Tesmer, V.M. / Lodowski, D.T. / Steinhagen, H. / Huber, J.
History
DepositionMar 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2012Group: Database references

-
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)125,5414
Polymers125,5163
Non-polymers241
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-44.6 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.736, 73.604, 122.914
Angle α, β, γ (deg.)90.000, 115.220, 90.000
Int Tables number5
Space group name H-MC121

-
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: ADRBK1, BARK, BARK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm)
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: 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
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.25
Details: 200 mM NaCl, 5% ethylene glycol, 6.3% PEG 3350, pH 5.25, vapor diffusion, hanging drop, temperature 277K, VAPOR DIFFUSION, HANGING DROP

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.033 Å
DetectorDetector: CCD / Date: Feb 23, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 38796 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.101 / Χ2: 1.286 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.75-2.850.54538400.635198.8
2.85-2.960.41638540.648199
2.96-3.10.33338780.773199.2
3.1-3.260.23138630.93199.5
3.26-3.460.15638941.049199.5
3.46-3.730.11838891.337199.3
3.73-4.110.09339091.649199.3
4.11-4.70.07338981.971199.5
4.7-5.920.06639551.838199.6
5.92-500.05638162.173194.3

-
Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
RefinementResolution: 2.75→25 Å / Cor.coef. Fo:Fc: 0.939 / SU B: 19.966 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / σ(F): 0 / ESU R: 0.668 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.269 1949 -
Rwork0.208 --
all0.208 38772 -
obs0.208 38772 98.79 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å2-2.18 Å2
2--3.35 Å20 Å2
3----4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 1 19 8185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228337
X-RAY DIFFRACTIONr_bond_other_d0.0010.025845
X-RAY DIFFRACTIONr_angle_refined_deg1.311.95711223
X-RAY DIFFRACTIONr_angle_other_deg0.86314168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63851013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01823.663404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.585151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4371567
X-RAY DIFFRACTIONr_chiral_restr0.0730.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021737
X-RAY DIFFRACTIONr_nbd_refined0.2160.21675
X-RAY DIFFRACTIONr_nbd_other0.1850.25871
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23932
X-RAY DIFFRACTIONr_nbtor_other0.0870.24525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2174
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.21
X-RAY DIFFRACTIONr_mcbond_it1.17226545
X-RAY DIFFRACTIONr_mcbond_other0.10522064
X-RAY DIFFRACTIONr_mcangle_it1.74358138
X-RAY DIFFRACTIONr_scbond_it2.89553834
X-RAY DIFFRACTIONr_scangle_it4.238103085
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 152 -
Rwork0.311 2780 -
obs-2780 97.58 %
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)
11.6168-0.10010.08882.19020.66253.87970.0193-0.1444-0.23250.2395-0.1960.01990.5964-0.00020.1767-0.0782-0.0589-0.1211-0.1472-0.0357-0.064243.261-5.27147.423
22.20150.0010.85561.04480.04012.5809-0.06430.13470.1827-0.06520.0657-0.1747-0.21020.3488-0.0014-0.0991-0.1120.0059-0.0954-0.0482-0.187567.11943.43113.012
32.11480.0637-0.34172.04610.0674.90830.11610.33420.3344-0.1558-0.1158-0.1041-0.47850.0406-0.0003-0.04690.0631-0.0601-0.0869-0.0446-0.130750.88529.33453.618
45.16110.45061.9023.53091.40737.27530.3342-0.4334-0.20440.3678-0.30880.20950.9071-0.8172-0.02540.031-0.14630.0226-0.0208-0.0955-0.314548.77123.42890.601
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA185 - 513185 - 513
2X-RAY DIFFRACTION1AD - E690 - 7001 - 10
3X-RAY DIFFRACTION2BB2 - 3402 - 340
4X-RAY DIFFRACTION2GC8 - 6814 - 74
5X-RAY DIFFRACTION2BF341 - 3421 - 2
6X-RAY DIFFRACTION2BF343 - 3473 - 7
7X-RAY DIFFRACTION3AA29 - 18429 - 184
8X-RAY DIFFRACTION3AA514 - 545514 - 545
9X-RAY DIFFRACTION3AE70111
10X-RAY DIFFRACTION4AA546 - 669546 - 669

+
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