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- PDB-4qj5: Structure of a fragment of human phospholipase C-beta3 delta472-5... -

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Basic information

Entry
Database: PDB / ID: 4qj5
TitleStructure of a fragment of human phospholipase C-beta3 delta472-581, 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 / forebrain neuron development / PLC beta mediated events / regulation of melanocyte differentiation / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Acetylcholine regulates insulin secretion / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) ...Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / forebrain neuron development / PLC beta mediated events / regulation of melanocyte differentiation / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Acetylcholine regulates insulin secretion / Thromboxane signalling through TP receptor / Thrombin signalling through proteinase activated receptors (PARs) / G-protein activation / G alpha (q) signalling events / PLC beta mediated events / phosphoinositide phospholipase C / endothelin receptor signaling pathway / developmental pigmentation / phospholipase C-activating dopamine receptor signaling pathway / cranial skeletal system development / phosphatidylinositol metabolic process / maternal behavior / ADP signalling through P2Y purinoceptor 1 / regulation of systemic arterial blood pressure / phospholipase C activity / phosphatidylinositol phospholipase C activity / multicellular organism aging / glutamate receptor signaling pathway / alkylglycerophosphoethanolamine phosphodiesterase activity / regulation of canonical Wnt signaling pathway / action potential / embryonic digit morphogenesis / neuron remodeling / postsynaptic cytosol / Synthesis of IP3 and IP4 in the cytosol / negative regulation of potassium ion transport / activation of phospholipase C activity / Presynaptic function of Kainate receptors / G beta:gamma signalling through PLC beta / phosphatidylinositol-mediated signaling / G-protein beta/gamma-subunit complex binding / lipid catabolic process / post-embryonic development / heterotrimeric G-protein complex / GTPase activator activity / positive regulation of smooth muscle cell proliferation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / skeletal system development / G protein-coupled receptor binding / caveola / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / negative regulation of protein kinase activity / regulation of blood pressure / cell body / G alpha (q) signalling events / heart development / nuclear membrane / calmodulin binding / protein stabilization / G protein-coupled receptor signaling pathway / cadherin binding / GTPase activity / synapse / dendrite / protein-containing complex binding / GTP binding / calcium ion binding / negative regulation of apoptotic process / Golgi apparatus / protein-containing complex / membrane / metal ion binding / plasma membrane / nucleus / cytosol
Similarity search - Function
PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / Phospholipase C-beta, C-terminal domain superfamily / PH domain / PLC-beta, PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide-specific phospholipase C, EF-hand-like domain ...PH-domain like - #240 / Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / Phospholipase C-beta, C-terminal domain superfamily / PH domain / PLC-beta, PH domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / G-protein alpha subunit, group Q / Phosphoinositide-specific phospholipase C, efhand-like / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phospholipase C, catalytic domain (part); domain Y / Phosphatidylinositol-specific phospholipase Y-box domain profile. / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / 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 / G-alpha domain profile. / G protein alpha subunit, helical insertion / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G protein alpha subunit / EF-hand / C2 domain superfamily / Recoverin; domain 1 / EF-hand domain pair / P-loop containing nucleotide triphosphate hydrolases / Roll / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / P-loop containing nucleoside triphosphate hydrolase / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(q) subunit alpha / TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / 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: 3.41 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

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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
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-44 kcal/mol
Surface area46440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.918, 89.869, 93.261
Angle α, β, γ (deg.)90.00, 101.80, 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: pFastBacHTA / 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, 7 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.: 2 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 100 mM MES, 200 mM NaCl, 5% (v/v) PEG 3350, pH 6.25, 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: 3.4→30 Å / Num. all: 27361 / Num. obs: 22003 / % possible obs: 96.1 % / Observed criterion σ(F): -2000 / Observed criterion σ(I): -2 / Redundancy: 3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.695
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.05 / % possible all: 95.9

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Processing

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

3ohm
PDB Unreleased entry


Resolution: 3.41→29.34 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.865 / SU B: 88.636 / SU ML: 0.602 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.626 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27671 1040 4.7 %RANDOM
Rwork0.21189 ---
obs0.21502 20962 95.49 %-
all-20962 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.894 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å2-0.03 Å2
2--1.69 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 3.41→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8621 0 59 2 8682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0198875
X-RAY DIFFRACTIONr_bond_other_d0.0010.028479
X-RAY DIFFRACTIONr_angle_refined_deg1.0161.9812007
X-RAY DIFFRACTIONr_angle_other_deg0.703319522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62351060
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35323.846429
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.665151583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.791571
X-RAY DIFFRACTIONr_chiral_restr0.0550.21319
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022041
X-RAY DIFFRACTIONr_mcbond_it0.8212.5884252
X-RAY DIFFRACTIONr_mcbond_other0.8212.5884251
X-RAY DIFFRACTIONr_mcangle_it1.5283.8785308
X-RAY DIFFRACTIONr_mcangle_other1.5283.8785309
X-RAY DIFFRACTIONr_scbond_it0.4472.6224623
X-RAY DIFFRACTIONr_scbond_other0.4452.624619
X-RAY DIFFRACTIONr_scangle_other0.8983.9136694
X-RAY DIFFRACTIONr_long_range_B_refined2.6419.7289840
X-RAY DIFFRACTIONr_long_range_B_other2.6419.7329841
LS refinement shellResolution: 3.41→3.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 71 -
Rwork0.299 1438 -
obs--90.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.31640.37610.50520.54740.15041.3506-0.06340.03720.14280.10140.07790.13780.16460.2476-0.01441.2630.1311-0.05770.6795-0.03640.04710.2408-4.355947.513
20.3321-0.01230.07730.0956-0.00531.2077-0.02580.02920.08-0.0445-0.06790.0398-0.11620.30580.09361.3232-0.1094-0.14740.6266-0.02840.055326.486410.042912.7198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 352
2X-RAY DIFFRACTION1A400 - 402
3X-RAY DIFFRACTION2B12 - 881
4X-RAY DIFFRACTION2B901
5X-RAY DIFFRACTION2B902

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