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- PDB-4qj4: Structure of a fragment of human phospholipase C-beta3 delta472-5... -

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Basic information

Entry
Database: PDB / ID: 4qj4
TitleStructure of a fragment of human phospholipase C-beta3 delta472-569, bound to IP3 and in complex with Galphaq
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
  • Guanine nucleotide-binding protein G(q) subunit alpha
KeywordsSIGNALING PROTEIN/HYDROLASE / GTP-BINDING PROTEIN ALPHA SUBUNITS / PHOSPHOLIPASE C BETA / PH DOMAIN / EF HAND / C2 DOMAIN / TIM BARREL DOMAIN / GTP HYDROLYSIS / G-PROTEIN SIGNALING / LIPASE / CALCIUM BINDING / GTP BINDING / PHOSPHOLIPIDS / membrane / SIGNALING PROTEIN-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 / 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 / Acetylcholine regulates insulin secretion / PLC beta mediated events / 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 / Acetylcholine regulates insulin secretion / 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 / developmental pigmentation / phosphatidylinositol metabolic process / PLC beta mediated events / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / regulation of platelet activation / ADP signalling through P2Y purinoceptor 1 / regulation of systemic arterial blood pressure / maternal behavior / phosphatidylinositol phospholipase C activity / phospholipase C activity / glutamate receptor signaling pathway / phosphatidylinositol-mediated signaling / regulation of canonical Wnt signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / postsynaptic cytosol / action potential / neuron remodeling / embryonic digit morphogenesis / Synthesis of IP3 and IP4 in the cytosol / ligand-gated ion channel signaling pathway / negative regulation of potassium ion transport / enzyme regulator activity / lipid catabolic process / release of sequestered calcium ion into cytosol / GTPase activator activity / post-embryonic development / G protein activity / skeletal system development / molecular function activator activity / G protein-coupled receptor binding / caveola / positive regulation of smooth muscle cell proliferation / 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 / positive regulation of insulin secretion / regulation of blood pressure / heterotrimeric G-protein complex / cell body / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / heart development / G alpha (q) signalling events / nuclear membrane / protein stabilization / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / dendrite / synapse / calcium ion binding / protein-containing complex binding / GTP binding / negative regulation of apoptotic process / Golgi apparatus / protein-containing complex / membrane / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / G-protein alpha subunit, group Q ...PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / 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 (PI) phosphodiesterase / Phosphatidylinositol-specific phospholipase X-box domain profile. / 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 / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / PH-domain like / EF-hand / Recoverin; domain 1 / C2 domain superfamily / 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 / EF-hand domain pair / P-loop containing nucleotide triphosphate hydrolases / Roll / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / 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: 3.3 Å
AuthorsLyon, A.M. / Tesmer, J.J.G.
CitationJournal: Structure / Year: 2014
Title: Molecular mechanisms of phospholipase C beta 3 autoinhibition.
Authors: Lyon, A.M. / Begley, J.A. / Manett, T.D. / Tesmer, J.J.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.4Sep 20, 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_ref_seq_dif / 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.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.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: 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)136,0367
Polymers135,0062
Non-polymers1,0315
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-42 kcal/mol
Surface area46200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.923, 89.191, 92.639
Angle α, β, γ (deg.)90.00, 101.70, 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: 44711.590 Da / Num. of mol.: 1 / Fragment: UNP residues 7-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gnaq / Plasmid: pFastBac HTA / Production host: TRICHOPLUSIA NI (cabbage looper) / 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: 90294.156 Da / Num. of mol.: 1 / Fragment: UNP residues 10-891
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Plasmid: pFastBacDual / Production host: TRICHOPLUSIA NI (cabbage looper)
References: UniProt: Q01970, phosphoinositide phospholipase C

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Non-polymers , 6 types, 17 molecules

#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Inositol trisphosphate


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM BisTris, 200 mM NaCl, 8% (v/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 18, 2014
RadiationMonochromator: KOHZU MONOCHROMATOR, CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 21343 / Num. obs: 21289 / % possible obs: 85.6 % / Observed criterion σ(F): -2000 / Observed criterion σ(I): -2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.221 / Net I/σ(I): 8.71
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.27 / % possible all: 64.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0049refinement
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0049phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OHM

3ohm
PDB Unreleased entry


Resolution: 3.3→29.4 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.851 / SU B: 62.713 / SU ML: 0.458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.614 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26665 1010 4.7 %RANDOM
Rwork0.2078 ---
obs0.21063 20279 85.14 %-
all-20279 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.06 Å2
2--0.41 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8646 0 59 12 8717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198900
X-RAY DIFFRACTIONr_bond_other_d0.0010.028493
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.9812041
X-RAY DIFFRACTIONr_angle_other_deg0.676319557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05451063
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12123.889432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.406151587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4971571
X-RAY DIFFRACTIONr_chiral_restr0.050.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022044
X-RAY DIFFRACTIONr_mcbond_it0.9264.5324264
X-RAY DIFFRACTIONr_mcbond_other0.9264.5334263
X-RAY DIFFRACTIONr_mcangle_it1.6866.7965323
X-RAY DIFFRACTIONr_mcangle_other1.6866.7965324
X-RAY DIFFRACTIONr_scbond_it0.6764.6024636
X-RAY DIFFRACTIONr_scbond_other0.6764.5994632
X-RAY DIFFRACTIONr_scangle_other1.2666.8716713
X-RAY DIFFRACTIONr_long_range_B_refined3.03635.1949945
X-RAY DIFFRACTIONr_long_range_B_other3.03635.1999946
LS refinement shellResolution: 3.3→3.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 45 -
Rwork0.25 1041 -
obs--59.31 %
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)
12.60241.14530.84061.77560.64382.79440.0213-0.14180.2661-0.0445-0.06760.1910.01450.1020.04630.04010.1072-0.01540.3223-0.05810.03810.3271-4.324946.6416
21.12160.038-0.00860.70310.111.998-0.10160.12120.2269-0.1320.01940.0713-0.24690.19970.08210.064-0.072-0.03450.2759-0.00910.061826.24169.900912.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 352
2X-RAY DIFFRACTION1A400 - 402
3X-RAY DIFFRACTION2B12 - 882
4X-RAY DIFFRACTION2B901
5X-RAY DIFFRACTION2B902

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