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- PDB-8jqi: Cryo EM map of full length PLC gamma 2 and FGFR1 Kinase Domain -

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Basic information

Entry
Database: PDB / ID: 8jqi
TitleCryo EM map of full length PLC gamma 2 and FGFR1 Kinase Domain
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
  • Fibroblast growth factor receptor 1
KeywordsHYDROLASE / PLCg2 / PLC gamma 2
Function / homology
Function and homology information


follicular B cell differentiation / inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process ...follicular B cell differentiation / inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / phosphoinositide phospholipase C / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / antifungal innate immune response / vitamin D3 metabolic process / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / positive regulation of interleukin-23 production / cellular response to lectin / response to yeast / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / response to sodium phosphate / auditory receptor cell development / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / phosphorylation-dependent protein binding / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / positive regulation of cell cycle G1/S phase transition / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of parathyroid hormone secretion / phosphatidylinositol metabolic process / mesenchymal cell proliferation / paraxial mesoderm development / positive regulation of phagocytosis, engulfment / positive regulation of neuroinflammatory response / cell activation / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / Erythropoietin activates Phospholipase C gamma (PLCG) / FGFR1c ligand binding and activation / phospholipase C activity / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / lung-associated mesenchyme development / phosphatidylinositol biosynthetic process / programmed cell death / cell projection assembly / macrophage activation involved in immune response / phospholipid catabolic process / cellular response to lipid / outer ear morphogenesis / embryonic limb morphogenesis / regulation of canonical NF-kappaB signal transduction / negative regulation of programmed cell death / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / skeletal system morphogenesis / positive regulation of mesenchymal cell proliferation / middle ear morphogenesis / positive regulation of macrophage cytokine production / ureteric bud development / cardiac muscle cell proliferation / inner ear morphogenesis / toll-like receptor signaling pathway / phosphatidylinositol-mediated signaling / positive regulation of reactive oxygen species biosynthetic process / PI-3K cascade:FGFR1 / midbrain development / intracellular vesicle / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / Dectin-2 family / positive regulation of NLRP3 inflammasome complex assembly / Synthesis of IP3 and IP4 in the cytosol / stimulatory C-type lectin receptor signaling pathway / Fc-epsilon receptor signaling pathway / fibroblast growth factor binding / B cell activation / regulation of cell differentiation / regulation of lipid metabolic process / positive regulation of interleukin-10 production / positive regulation of receptor internalization / Generation of second messenger molecules / PI3K Cascade / positive regulation of epithelial cell migration / cellular response to fibroblast growth factor stimulus / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / positive regulation of type I interferon production / response to axon injury / Role of phospholipids in phagocytosis
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / PLCG EF-hand motif 2 / Pleckstrin homology domain / Fibroblast growth factor receptor 1, catalytic domain / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / PLCG EF-hand motif 2 / Pleckstrin homology domain / Fibroblast growth factor receptor 1, catalytic domain / 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 / Fibroblast growth factor receptor family / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / : / SH3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain pair / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Fibroblast growth factor receptor 1 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsShin, Y.-C. / Liao, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Sci Adv / Year: 2024
Title: The crystal and cryo-EM structures of PLCγ2 reveal dynamic interdomain recognitions in autoinhibition.
Authors: Young-Cheul Shin / Ashlee Marie Plummer-Medeiros / Alison Mungenast / Hyeong-Wook Choi / Karen TenDyke / Xiaojie Zhu / Jennifer Shepard / Kristen Sanders / Ningning Zhuang / Liang Hu / ...Authors: Young-Cheul Shin / Ashlee Marie Plummer-Medeiros / Alison Mungenast / Hyeong-Wook Choi / Karen TenDyke / Xiaojie Zhu / Jennifer Shepard / Kristen Sanders / Ningning Zhuang / Liang Hu / Dongming Qian / Kangkang Song / Chen Xu / John Wang / Suresh B Poda / Maofu Liao / Yu Chen /
Abstract: Phospholipase C gamma 2 (PLCγ2) plays important roles in cell signaling downstream of various membrane receptors. PLCγ2 contains a multidomain inhibitory region critical for its regulation, while ...Phospholipase C gamma 2 (PLCγ2) plays important roles in cell signaling downstream of various membrane receptors. PLCγ2 contains a multidomain inhibitory region critical for its regulation, while it has remained unclear how these domains contribute to PLCγ2 activity modulation. Here we determined three structures of human PLCγ2 in autoinhibited states, which reveal dynamic interactions at the autoinhibition interface, involving the conformational flexibility of the Src homology 3 (SH3) domain in the inhibitory region, and its previously unknown interaction with a carboxyl-terminal helical domain in the core region. We also determined a structure of PLCγ2 bound to the kinase domain of fibroblast growth factor receptor 1 (FGFR1), which demonstrates the recognition of FGFR1 by the nSH2 domain in the inhibitory region of PLCγ2. Our results provide structural insights into PLCγ2 regulation that will facilitate future mechanistic studies to understand the entire activation process.
#1: Journal: Biorxiv / Year: 2023
Title: The crystal and cryo-EM structures of PLC gamma 2 reveal dynamic inter-domain recognitions in autoinhibition
Authors: Shin, Y.C. / Plummer-Medeiros, A.M. / Mungenast, A. / Choi, H.W. / TenDyke, K. / Zhu, X. / Shepard, J. / Zhuang, N. / Hu, L. / Qian, D. / Song, K. / Xu, C. / Wang, J. / Poda, S.B. / Liao, M. / Chen, Y.
History
DepositionJun 14, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
B: Fibroblast growth factor receptor 1


Theoretical massNumber of molelcules
Total (without water)240,0532
Polymers240,0532
Non-polymers00
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 gamma-2 / Phosphoinositide phospholipase C-gamma-2 / Phospholipase C-IV / PLC-IV / Phospholipase C-gamma-2 / PLC-gamma-2


Mass: 148074.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCG2 / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P16885, phosphoinositide phospholipase C
#2: Protein Fibroblast growth factor receptor 1 / FGFR-1 / Basic fibroblast growth factor receptor 1 / BFGFR / bFGF-R-1 / Fms-like tyrosine kinase 2 ...FGFR-1 / Basic fibroblast growth factor receptor 1 / BFGFR / bFGF-R-1 / Fms-like tyrosine kinase 2 / FLT-2 / N-sam / Proto-oncogene c-Fgr


Mass: 91978.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
References: UniProt: P11362, receptor protein-tyrosine kinase
Has protein modificationN

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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: PLCg2 and FGFR1 / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.1478 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293F
Buffer solutionpH: 7.9 / Details: 25 mM Tris pH 7.9, 150 mM NaCl, 1mM TCEP
SpecimenConc.: 2.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 53.0932 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45439 / Symmetry type: POINT

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