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- PDB-2bcj: Crystal Structure of G Protein-Coupled Receptor Kinase 2 in Compl... -

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Basic information

Entry
Database: PDB / ID: 2bcj
TitleCrystal Structure of G Protein-Coupled Receptor Kinase 2 in Complex with Galpha-q and Gbetagamma Subunits
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • G-protein-coupled receptor kinase 2
KeywordsTRANSFERASE/HYDROLASE / Peripheral membrane complex / protein kinase / RGS domain / WD40 protein / heterotrimeric G protein / TRANSFERASE-HYDROLASE COMPLEX
Function / homology
Function and homology information


Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / PLC beta mediated events / forebrain neuron development / regulation of melanocyte differentiation / Calmodulin induced events / beta-adrenergic-receptor kinase / negative regulation of the force of heart contraction by chemical signal / negative regulation of relaxation of smooth muscle / Activation of SMO / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / Thrombin signalling through proteinase activated receptors (PARs) / Edg-2 lysophosphatidic acid receptor binding / alpha-2A adrenergic receptor binding / Extra-nuclear estrogen signaling / G-protein activation / Adenylate cyclase inhibitory pathway / G alpha (q) signalling events / endothelin receptor signaling pathway / ion channel modulating, G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Olfactory Signaling Pathway / developmental pigmentation / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / negative regulation of striated muscle contraction / desensitization of G protein-coupled receptor signaling pathway / positive regulation of protein localization to cilium / Cargo recognition for clathrin-mediated endocytosis / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / ADP signalling through P2Y purinoceptor 1 / regulation of platelet activation / regulation of the force of heart contraction / Activation of the phototransduction cascade / maternal behavior / positive regulation of smoothened signaling pathway / G protein-coupled receptor internalization / Adrenaline,noradrenaline inhibits insulin secretion / ADP signalling through P2Y purinoceptor 12 / glutamate receptor signaling pathway / GTPase activating protein binding / negative regulation of synaptic transmission / G alpha (i) signalling 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 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / alkylglycerophosphoethanolamine phosphodiesterase activity / 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 / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / action potential / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / neuron remodeling / embryonic digit morphogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / regulation of signal transduction / positive regulation of protein localization to cell cortex / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / cardiac muscle contraction / enzyme regulator activity / regulation of mitotic spindle organization / cellular response to forskolin / GTPase activator activity / post-embryonic development / G protein activity / skeletal system development / caveola / cell projection / G protein-coupled receptor binding / positive regulation of smooth muscle cell proliferation / intracellular protein transport / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion
Similarity search - Function
Helix Hairpins - #1270 / G-protein alpha subunit, group Q / 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Regulator of G protein signaling domain ...Helix Hairpins - #1270 / G-protein alpha subunit, group Q / 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 / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / 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. / G-protein alpha subunit, group I / 7 Propeller / Methylamine Dehydrogenase; Chain H / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / 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 / P-loop containing nucleotide triphosphate hydrolases / WD40 repeat, conserved site / Roll / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Beta-adrenergic receptor kinase 1 / Guanine nucleotide-binding protein G(q) subunit alpha / 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 (cattle)
Rattus norvegicus (Norway rat)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.061 Å
AuthorsTesmer, J.J.G.
CitationJournal: Science / Year: 2005
Title: Snapshot of Activated G Proteins at the Membrane: The Gq-GRK2-G Complex
Authors: Tesmer, V.M. / Kawano, T. / Shankaranarayanan, A. / Kozasa, T. / Tesmer, J.J.G.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.4Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G-protein-coupled receptor kinase 2
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
Q: Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,7767
Polymers166,2064
Non-polymers5703
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.918, 129.954, 122.764
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 79749.922 Da / Num. of mol.: 1 / Fragment: residues 28-689 / Mutation: S670A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GRK2, ADRBK1 / Plasmid: pVL1392 / Cell line (production host): High-5 cells / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P21146, beta-adrenergic-receptor kinase

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules BGQ

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 37311.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: GNB1 / Plasmid: pVL1393 / Cell line (production host): High-5 cells / Production host: Trichoplusia ni (cabbage looper) / 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 / Plasmid: pVL1392 / Cell line (production host): High-5 cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P63212
#4: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1, Guanine nucleotide-binding protein G(q) subunit alpha chimera / Adenylate cyclase-inhibiting G alpha protein / Guanine nucleotide-binding protein alpha-q


Mass: 41298.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse)
Genus: Rattus, Mus / Species: , / Gene: Gnai1, Gnai-1, Gnaq / Plasmid: pFastBacHTA / Cell line (production host): High-5 cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P10824, UniProt: P21279

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Non-polymers , 4 types, 8 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 3.22 Å3/Da / Density % sol: 61.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 9% PEG8000, 1M NaCl, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.06→46.78 Å / Num. all: 37836 / Num. obs: 37836 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.7 % / Biso Wilson estimate: 75 Å2 / Rsym value: 0.133 / Net I/σ(I): 13.55
Reflection shellResolution: 3.06→3.21 Å / Mean I/σ(I) obs: 1.1 / Num. unique all: 3738 / Rsym value: 0.849 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OMW, homology model of Galphaq

1omw


Resolution: 3.061→46.78 Å / Cor.coef. Fo:Fc: 0.943 / SU B: 50.535 / SU ML: 0.343 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Rfree was not used for the last three rounds of refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1900 -Random
Rwork0.243 ---
all0.236 38314 --
obs0.236 37811 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.36 Å2
2--5.78 Å20 Å2
3----5.27 Å2
Refinement stepCycle: LAST / Resolution: 3.061→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10839 0 34 5 10878
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211104
X-RAY DIFFRACTIONr_bond_other_d0.0010.029987
X-RAY DIFFRACTIONr_angle_refined_deg0.9171.96114976
X-RAY DIFFRACTIONr_angle_other_deg0.681323268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54451339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92623.849543
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.653152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3891584
X-RAY DIFFRACTIONr_chiral_restr0.0530.21622
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212257
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022309
X-RAY DIFFRACTIONr_nbd_refined0.1860.22358
X-RAY DIFFRACTIONr_nbd_other0.1550.210527
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25335
X-RAY DIFFRACTIONr_nbtor_other0.0780.26679
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.0710.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1060.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1260.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.25
X-RAY DIFFRACTIONr_mcbond_it0.7128748
X-RAY DIFFRACTIONr_mcbond_other0.03522722
X-RAY DIFFRACTIONr_mcangle_it0.817410790
X-RAY DIFFRACTIONr_scbond_it0.97565225
X-RAY DIFFRACTIONr_scangle_it1.41684186
LS refinement shellResolution: 3.061→3.141 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.397 2363 -
obs-2363 83.68 %
Refinement TLS params.Method: refined / Origin x: 16.358 Å / Origin y: -1.5957 Å / Origin z: 6.6176 Å
111213212223313233
T0.0081 Å2-0.0443 Å20.005 Å2-0.2777 Å20.0451 Å2---0.2513 Å2
L0.4074 °20.004 °2-0.0396 °2-0.1177 °20.2395 °2--0.4931 °2
S-0.0149 Å °-0.0433 Å °-0.041 Å °-0.0076 Å °0.0771 Å °-0.0527 Å °0.0447 Å °0.1079 Å °-0.0623 Å °
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Selection: ALL

IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1AA28 - 66728 - 667
2BB1 - 3401 - 339
3GC4 - 674 - 67
4QD38 - 35432 - 348

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