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- PDB-9b13: Cryo-EM structure of phospholipase Cepsilon PH-COOH in complex wi... -

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Basic information

Entry
Database: PDB / ID: 9b13
TitleCryo-EM structure of phospholipase Cepsilon PH-COOH in complex with an antigen-binding fragment (composite structure)
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
  • Antigen-binding fragment heavy chain
  • Antigen-binding fragment light chain
KeywordsMEMBRANE PROTEIN / phospholipase c / antigen-binding fragment / complex
Function / homology
Function and homology information


diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling / lipid catabolic process / positive regulation of lamellipodium assembly ...diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / glomerulus development / phosphatidylinositol-mediated signaling / lipid catabolic process / positive regulation of lamellipodium assembly / release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / small GTPase binding / epidermal growth factor receptor signaling pathway / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / enzyme binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / 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 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / 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 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / 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. / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / 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 / EF-hand domain pair / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsSamassekou, K. / Lyon, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL141076-01 United States
American Heart Association23PRE1011279 United States
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM structure of phospholipase Cε defines N-terminal domains and their roles in activity.
Authors: Kadidia Samassekou / Elisabeth E Garland-Kuntz / Vaani Ohri / Isaac J Fisher / Satchal K Erramilli / Kaushik Muralidharan / Livia M Bogdan / Abigail M Gick / Anthony Kossiakoff / Angeline M Lyon /
Abstract: Phospholipase Cε (PLCε) increases intracellular Ca and protein kinase C (PKC) activity in the cardiovascular system in response to stimulation of G protein coupled receptors (GPCRs) and receptor ...Phospholipase Cε (PLCε) increases intracellular Ca and protein kinase C (PKC) activity in the cardiovascular system in response to stimulation of G protein coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). The ability of PLCε to respond to these diverse inputs is due, in part, to multiple, conformationally dynamic regulatory domains. However, this heterogeneity has limited structural studies of the lipase to either individual domains or its catalytic core. Here, we report the 3.9 Å reconstruction of the largest fragment of PLCε to date in complex with an antigen binding fragment (Fab). The structure reveals that PLCε contains a pleckstrin homology (PH) domain and four tandem EF hands, including subfamily-specific insertions and intramolecular interactions with the catalytic core. The structure, together with a model of the holoenzyme, suggest that part of the N-terminus and PH domain may form a surface that supports lipase activity. Functional characterization of this surface confirms it is critical for maximum basal and G protein-stimulated activities. This study provides new insights into the autoinhibited, basal conformation of PLCε and how the N-terminal domains contribute to activity.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
H: Antigen-binding fragment heavy chain
L: Antigen-binding fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,3844
Polymers219,3433
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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


Mass: 165314.125 Da / Num. of mol.: 1 / Fragment: PH-C terminus, residues 837-2281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plce1, Plce / Plasmid: pFastBacHTA / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q99P84, phosphoinositide phospholipase C
#2: Antibody Antigen-binding fragment heavy chain


Mass: 28234.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#3: Antibody Antigen-binding fragment light chain


Mass: 25794.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Fab2-rPLCe PH-CCOMPLEXfragment of phospholipase C epsilon (residues 837-2281) in complex with an antigen binding fragment (Fab2)#1-#30MULTIPLE SOURCES
2rPLCe PH-CCOMPLEX#11RECOMBINANT
3Fab2COMPLEX#2-#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.214 MDaNO
210.165 MDaNO
310.489 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Rattus norvegicus (Norway rat)10116
23Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrainPlasmid
12Spodoptera frugiperda (fall armyworm)7108pFastBacHTA
23Escherichia coli (E. coli)562BL21pRH 2.2
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMsodium chlorideNaCl1
30.3 mMtris(2-carboxyethyl)phosphineTCEP1
40.1 mMEthylenediaminetetraacetic acidEDTA1
50.1 mMegtazic acidEGTA1
60.005 %n-dodecyl-b-D-maltosideDDM1
SpecimenConc.: 0.6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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 magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.2 sec. / Electron dose: 53.75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7052

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1471782
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147120 / Symmetry type: POINT

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