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- PDB-7sq2: Reprocessed and refined structure of Phospholipase C-beta and Gq ... -

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Basic information

Entry
Database: PDB / ID: 7sq2
TitleReprocessed and refined structure of Phospholipase C-beta and Gq signaling complex
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
  • Guanine nucleotide-binding protein G(q) subunit alpha
KeywordsSIGNALING PROTEIN / G-protein signaling Phopholipase-C Hydrolase Guanine nucleotide-binding protein G(q) alpha
Function / homology
Function and homology information


Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / PLC beta mediated events / Acetylcholine regulates insulin secretion / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / PLC beta mediated events / Acetylcholine regulates insulin secretion / forebrain neuron development / regulation of melanocyte differentiation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / phosphoinositide phospholipase C / : / phospholipase C-activating G protein-coupled acetylcholine receptor signaling pathway / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Acetylcholine regulates insulin secretion / G alpha (q) signalling events / endothelin receptor signaling pathway / phospholipase C-activating dopamine receptor signaling pathway / developmental pigmentation / phospholipase C-activating serotonin receptor signaling pathway / PLC beta mediated events / phosphatidylinositol metabolic process / regulation of systemic arterial blood pressure / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cranial skeletal system development / ADP signalling through P2Y purinoceptor 1 / regulation of platelet activation / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / maternal behavior / glutamate receptor signaling pathway / embryonic digit morphogenesis / neuron remodeling / phosphatidylinositol-mediated signaling / Synthesis of IP3 and IP4 in the cytosol / ligand-gated ion channel signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / action potential / postsynaptic cytosol / lipid catabolic process / enzyme regulator activity / release of sequestered calcium ion into cytosol / molecular function activator activity / post-embryonic development / skeletal system development / G protein-coupled receptor binding / positive regulation of insulin secretion / regulation of blood pressure / G-protein beta/gamma-subunit complex binding / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / adenylate cyclase-activating G protein-coupled receptor signaling pathway / heterotrimeric G-protein complex / G protein activity / heart development / cell body / Ca2+ pathway / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / phospholipase C-activating G protein-coupled receptor signaling pathway / molecular adaptor activity / nuclear membrane / G alpha (q) signalling events / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / calcium ion binding / GTP binding / Golgi apparatus / protein-containing complex / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family ...Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / Phosphatidylinositol-specific phospholipase X-box domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Guanine nucleotide-binding protein G(q) subunit alpha / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEndo-Streeter, S.T. / Sondek, J. / Harden, T.K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM38213 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM57391 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM61454 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM074001 United States
National Institutes of Health/National Eye Institute (NIH/NEI)EY010582 United States
CitationJournal: Science / Year: 2010
Title: Kinetic Scaffolding Mediated by a Phospholipase C-{beta} and Gq Signaling Complex
Authors: Endo-Streeter, S.T. / Sondek, J. / Harden, T.K.
History
DepositionNov 4, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionNov 17, 2021ID: 3OHM
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide-binding protein G(q) subunit alpha
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,17014
Polymers138,1222
Non-polymers1,04812
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-53 kcal/mol
Surface area47110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.837, 90.817, 93.135
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Guanine nucleotide-binding protein G(q) subunit alpha / Guanine nucleotide-binding protein alpha-q


Mass: 38256.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21279
#2: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 / Phosphoinositide phospholipase C-beta-3 / Phospholipase C-beta-3 / PLC-beta-3


Mass: 99865.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q01970, phosphoinositide phospholipase C

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Non-polymers , 6 types, 227 molecules

#3: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 7% PEG 6000, 100 mM Hepes, 1 mM CaCl2, 100 mM magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2010 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagittally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→40.55 Å / Num. obs: 48454 / % possible obs: 99.49 % / Redundancy: 5.6 % / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Χ2: 1.804 / Net I/σ(I): 32.5
Reflection shellResolution: 2.6→2.666 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2.67 / Num. unique obs: 2555 / CC1/2: 0.905 / CC star: 0.975 / Rpim(I) all: 0.304 / Rrim(I) all: 0.723 / Χ2: 0.957 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OHM

3ohm
PDB Unreleased entry


Resolution: 2.6→40.55 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 29.23 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.444 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26334 2571 5 %RANDOM
Rwork0.19924 ---
obs0.20247 48454 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 91.472 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20.51 Å2
2--5.24 Å2-0 Å2
3----6.06 Å2
Refinement stepCycle: 1 / Resolution: 2.6→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8678 0 64 215 8957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0138920
X-RAY DIFFRACTIONr_bond_other_d00.0178322
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.65612069
X-RAY DIFFRACTIONr_angle_other_deg0.9591.57619316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.43451068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.07822.008503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.139151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3191570
X-RAY DIFFRACTIONr_chiral_restr0.0560.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0340.029875
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9793.7994291
X-RAY DIFFRACTIONr_mcbond_other4.9383.7884283
X-RAY DIFFRACTIONr_mcangle_it7.0545.6785348
X-RAY DIFFRACTIONr_mcangle_other7.0545.6785349
X-RAY DIFFRACTIONr_scbond_it5.9594.2394629
X-RAY DIFFRACTIONr_scbond_other5.964.244630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3586.1846722
X-RAY DIFFRACTIONr_long_range_B_refined12.74145.289963
X-RAY DIFFRACTIONr_long_range_B_other12.74145.299964
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å
RfactorNum. reflection% reflection
Rfree0.34 203 -
Rwork0.274 3414 -
obs--95.59 %
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)
13.17490.5215-0.08121.55980.4333.2123-0.0331-0.13990.24020.14640.1612-0.00930.45630.5576-0.12810.7130.2249-0.52470.1395-0.14220.416910.727-4.54547.517
21.4566-0.2908-0.30390.8371-0.06183.60490.0751-0.03310.3093-0.2237-0.00260.0532-0.31060.4991-0.07250.62670.0189-0.48810.1446-0.11570.53926.68810.15713.269
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 353
2X-RAY DIFFRACTION2B12 - 880

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