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- PDB-8emv: Phospholipase C beta 3 (PLCb3) in solution -

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Basic information

Entry
Database: PDB / ID: 8emv
TitlePhospholipase C beta 3 (PLCb3) in solution
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
KeywordsHYDROLASE / PIP2 degradation / IP3 production / DAG production / G protein signaling
Function / homology
Function and homology information


phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phospholipase C-activating serotonin receptor signaling pathway / PLC beta mediated events / phosphatidylinositol metabolic process / regulation of systemic arterial blood pressure / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phosphatidylinositol-mediated signaling ...phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phospholipase C-activating serotonin receptor signaling pathway / PLC beta mediated events / phosphatidylinositol metabolic process / regulation of systemic arterial blood pressure / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phosphatidylinositol-mediated signaling / Synthesis of IP3 and IP4 in the cytosol / postsynaptic cytosol / lipid catabolic process / release of sequestered calcium ion into cytosol / molecular function activator activity / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (q) signalling events / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / calcium ion binding / protein-containing complex / nucleus / membrane / cytoplasm / cytosol
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 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain ...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 / 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 / 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. / EF-hand / Recoverin; domain 1 / C2 domain superfamily / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsFalzone, M.E. / MacKinnon, R.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM142137 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: activates hydrolysis by recruiting and orienting on the membrane surface.
Authors: Maria E Falzone / Roderick MacKinnon /
Abstract: catalyze the hydrolysis of phosphatidylinositol 4, 5-bisphosphate [Formula: see text] into [Formula: see text] [Formula: see text] and [Formula: see text]  [Formula: see text]. [Formula: see text] ... catalyze the hydrolysis of phosphatidylinositol 4, 5-bisphosphate [Formula: see text] into [Formula: see text] [Formula: see text] and [Formula: see text]  [Formula: see text]. [Formula: see text] regulates the activity of many membrane proteins, while and lead to increased intracellular Ca levels and activate protein kinase C, respectively. are regulated by G protein-coupled receptors through direct interaction with [Formula: see text] and [Formula: see text] and are aqueous-soluble enzymes that must bind to the cell membrane to act on their lipid substrate. This study addresses the mechanism by which [Formula: see text] activates 3. We show that 3 functions as a slow Michaelis-Menten enzyme ( [Formula: see text] ) on membrane surfaces. We used membrane partitioning experiments to study the solution-membrane localization equilibrium of 3. Its partition coefficient is such that only a small quantity of 3 exists in the membrane in the absence of [Formula: see text] . When [Formula: see text] is present, equilibrium binding on the membrane surface increases 3 in the membrane, increasing [Formula: see text] in proportion. Atomic structures on membrane vesicle surfaces show that two [Formula: see text] anchor 3 with its catalytic site oriented toward the membrane surface. Taken together, the enzyme kinetic, membrane partitioning, and structural data show that [Formula: see text] activates by increasing its concentration on the membrane surface and orienting its catalytic core to engage [Formula: see text] . This principle of activation explains rapid stimulated catalysis with low background activity, which is essential to the biological processes mediated by [Formula: see text], and .
History
DepositionSep 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,8712
Polymers138,8301
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 / Phosphoinositide phospholipase C-beta-3 / Phospholipase C-beta-3 / PLC-beta-3


Mass: 138830.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCB3 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q01970, phosphoinositide phospholipase C
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PLCb3 in solution / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.138 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenConc.: 4.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 289 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 42.87 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3527
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
4CTFFIND4CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1021849 / Details: picked with 2D templates
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67716 / Symmetry type: POINT

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