[English] 日本語
Yorodumi
- PDB-3psc: Bovine GRK2 in complex with Gbetagamma subunits -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3psc
TitleBovine GRK2 in complex with Gbetagamma subunits
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 / Kinase / Serine/threonine-protein kinase / ATP-binding / Membrane / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / 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 ...Calmodulin induced events / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / beta-adrenergic-receptor kinase / Activation of SMO / 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) / Cargo recognition for clathrin-mediated endocytosis / positive regulation of protein localization to cilium / 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 / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / 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 / regulation of signal transduction / cardiac muscle contraction / adenylate cyclase-activating adrenergic receptor signaling pathway / viral genome replication / cell projection / intracellular protein transport / G protein-coupled receptor binding / 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 / sensory perception of taste / presynapse / signaling receptor complex adaptor activity / heart development / retina development in camera-type eye / GTPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / cell population proliferation / protein phosphorylation / protein kinase activity / postsynapse / 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
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsThal, D.M. / Tesmer, J.J.
CitationJournal: Mol.Pharmacol. / Year: 2011
Title: Molecular Mechanism of Selectivity among G Protein-Coupled Receptor Kinase 2 Inhibitors.
Authors: Thal, D.M. / Yeow, R.Y. / Schoenau, C. / Huber, J. / Tesmer, J.J.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
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


Theoretical massNumber of molelcules
Total (without water)126,4023
Polymers126,4023
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-49 kcal/mol
Surface area48290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.928, 73.152, 122.780
Angle α, β, γ (deg.)90.00, 115.42, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Beta-adrenergic receptor kinase 1 / GRK2 / Beta-ARK-1 / G-protein-coupled receptor kinase 2


Mass: 80578.820 Da / Num. of mol.: 1 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ADRBK1, GRK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21146, 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: 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 / Fragment: UNP residues 1-68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 59.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG3350, 200 mM NaCl, 100 mM MES pH 6.5, 1 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 115 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 2, 2009
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 43102 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.073 / Net I/σ(I): 15.7
Reflection shellResolution: 2.67→2.76 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 4259 / Rsym value: 0.585 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMW

1omw


Resolution: 2.67→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 31.415 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 2165 5 %RANDOM
Rwork0.22278 ---
obs0.22453 40908 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.174 Å2
Baniso -1Baniso -2Baniso -3
1--5.07 Å20 Å2-5.48 Å2
2--7.29 Å20 Å2
3----6.93 Å2
Refinement stepCycle: LAST / Resolution: 2.67→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 0 0 8 8133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228293
X-RAY DIFFRACTIONr_bond_other_d0.0010.025807
X-RAY DIFFRACTIONr_angle_refined_deg1.161.95811171
X-RAY DIFFRACTIONr_angle_other_deg0.813314088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26351008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09823.734399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.332151513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4561564
X-RAY DIFFRACTIONr_chiral_restr0.0630.21207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021720
X-RAY DIFFRACTIONr_mcbond_it0.3631.55040
X-RAY DIFFRACTIONr_mcbond_other0.0541.52053
X-RAY DIFFRACTIONr_mcangle_it0.69128104
X-RAY DIFFRACTIONr_scbond_it0.95733253
X-RAY DIFFRACTIONr_scangle_it1.5974.53067
LS refinement shellResolution: 2.665→2.734 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.422 154 -
Rwork0.32 2955 -
obs-2955 98.01 %
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)
12.39520.8143-0.54271.5149-1.32646.6646-0.03280.3710.4345-0.0406-0.07470.0099-0.2501-0.33540.10740.35720.0514-0.04590.1911-0.04280.33451.604629.138753.4126
23.4725-0.44970.93952.93890.55195.28570.2974-0.2448-0.81070.4848-0.2494-0.20130.8794-0.1281-0.0480.5638-0.0993-0.26620.1379-0.07610.664545.3575-5.287345.22
36.05571.72982.6884.72752.696911.30670.4157-0.3837-0.37970.3897-0.18210.26481.3247-0.9784-0.23370.4102-0.15980.06190.3233-0.10720.168849.927323.037589.9701
44.06990.07731.98181.63550.57934.0402-0.14560.3510.1844-0.05190.2744-0.2663-0.22911.0685-0.12890.1189-0.10250.08220.3194-0.10520.1667.878343.8367112.149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 184
2X-RAY DIFFRACTION1A514 - 545
3X-RAY DIFFRACTION2A185 - 513
4X-RAY DIFFRACTION3A546 - 668
5X-RAY DIFFRACTION4B3 - 340
6X-RAY DIFFRACTION4G8 - 68

+
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