[English] 日本語
Yorodumi
- PDB-8jqi: Cryo EM map of full length PLC gamma 2 and FGFR1 Kinase Domain -

+
Open data


ID or keywords:

Loading...

-
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


inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / follicular B cell differentiation / 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 / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions ...inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / follicular B cell differentiation / 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 / diphosphate metabolic process / Signaling by plasma membrane FGFR1 fusions / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / phosphoinositide phospholipase C / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / vitamin D3 metabolic process / antifungal innate immune response / cementum mineralization / cellular response to lectin / regulation of phosphate transport / positive regulation of interleukin-23 production / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / Epithelial-Mesenchymal Transition (EMT) during gastrulation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / phosphorylation-dependent protein binding / mesenchymal cell proliferation / positive regulation of phospholipase activity / phosphatidylinositol metabolic process / receptor-receptor interaction / chordate embryonic development / positive regulation of cell cycle G1/S phase transition / positive regulation of parathyroid hormone secretion / Toll Like Receptor 4 (TLR4) Cascade / auditory receptor cell development / response to yeast / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / paraxial mesoderm development / cell activation / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / Erythropoietin activates Phospholipase C gamma (PLCG) / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade: FGFR1 / branching involved in salivary gland morphogenesis / C-type glycerophospholipase activity / positive regulation of phagocytosis, engulfment / phosphatidylinositol biosynthetic process / lung-associated mesenchyme development / programmed cell death / cell projection assembly / macrophage activation involved in immune response / phospholipid catabolic process / outer ear morphogenesis / cellular response to lipid / regulation of canonical NF-kappaB signal transduction / embryonic limb morphogenesis / positive regulation of endothelial cell chemotaxis / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / positive regulation of macrophage cytokine production / skeletal system morphogenesis / inner ear morphogenesis / negative regulation of programmed cell death / positive regulation of neuroinflammatory response / toll-like receptor signaling pathway / middle ear morphogenesis / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / Dectin-2 family / PI-3K cascade:FGFR1 / stimulatory C-type lectin receptor signaling pathway / midbrain development / Fc-epsilon receptor signaling pathway / positive regulation of MAP kinase activity / phosphatidylinositol-mediated signaling / Synthesis of IP3 and IP4 in the cytosol / intracellular vesicle / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / regulation of cell differentiation / fibroblast growth factor binding / regulation of lipid metabolic process / Generation of second messenger molecules / positive regulation of intracellular signal transduction / B cell activation / positive regulation of epithelial cell migration / positive regulation of receptor internalization / positive regulation of interleukin-10 production / fibroblast growth factor receptor signaling pathway / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / chondrocyte differentiation / 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 1 / PLCG EF-hand motif 2 / Pleckstrin homology domain / Fibroblast growth factor receptor 1, catalytic 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 1 / 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 / Src homology 3 domains / SH2 domain superfamily / 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. / Immunoglobulin subtype / Immunoglobulin / PH-like domain superfamily / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more