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- EMDB-36571: Cryo EM map of full length PLC gamma 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-36571
TitleCryo EM map of full length PLC gamma 2
Map dataEM map of PLC gamma 2
Sample
  • Complex: PLCg2 and FGFR1
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
KeywordsPLCg2 / PLC gamma 2 / HYDROLASE
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 / phosphoinositide phospholipase C / antifungal innate immune response / positive regulation of interleukin-23 production / cellular response to lectin / response to yeast / phosphorylation-dependent protein binding ...follicular B cell differentiation / inositol trisphosphate biosynthetic process / regulation of calcineurin-NFAT signaling cascade / positive regulation of dendritic cell cytokine production / phosphoinositide phospholipase C / antifungal innate immune response / positive regulation of interleukin-23 production / cellular response to lectin / response to yeast / phosphorylation-dependent protein binding / positive regulation of cell cycle G1/S phase transition / Toll Like Receptor 4 (TLR4) Cascade / phosphatidylinositol metabolic process / positive regulation of phagocytosis, engulfment / positive regulation of neuroinflammatory response / cell activation / Erythropoietin activates Phospholipase C gamma (PLCG) / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phosphatidylinositol biosynthetic process / programmed cell death / macrophage activation involved in immune response / phospholipid catabolic process / cellular response to lipid / regulation of canonical NF-kappaB signal transduction / negative regulation of programmed cell death / positive regulation of macrophage cytokine production / toll-like receptor signaling pathway / phosphatidylinositol-mediated signaling / positive regulation of reactive oxygen species biosynthetic process / intracellular vesicle / 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 / B cell activation / regulation of lipid metabolic process / positive regulation of interleukin-10 production / positive regulation of receptor internalization / Generation of second messenger molecules / positive regulation of epithelial cell migration / positive regulation of type I interferon production / response to axon injury / Role of phospholipids in phagocytosis / GPVI-mediated activation cascade / release of sequestered calcium ion into cytosol / phosphotyrosine residue binding / positive regulation of interleukin-12 production / FCERI mediated Ca+2 mobilization / positive regulation of interleukin-2 production / B cell differentiation / FCGR3A-mediated IL10 synthesis / positive regulation of calcium-mediated signaling / cellular response to calcium ion / lipopolysaccharide-mediated signaling pathway / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of DNA-binding transcription factor activity / protein tyrosine kinase binding / B cell receptor signaling pathway / FCERI mediated MAPK activation / calcium-mediated signaling / platelet activation / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / Wnt signaling pathway / ruffle membrane / Signaling by CSF1 (M-CSF) in myeloid cells / positive regulation of tumor necrosis factor production / DAP12 signaling / T cell receptor signaling pathway / scaffold protein binding / Potential therapeutics for SARS / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane / cytosol / cytoplasm
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 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain / Phosphatidylinositol-specific phospholipase Y-box domain profile. ...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 / 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. / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / 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 / PH-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsShin Y-C / Liao M
Funding support1 items
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 YC / Plummer-Medeiros AM / Mungenast A / Choi HW / TenDyke K / Zhu X / Shepard J / Zhuang N / Hu L / Qian D / Song K / Xu C / Wang J / Poda SB / Liao M / Chen Y
History
DepositionJun 14, 2023-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36571.png

Downloads & links

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Map

FileDownload / File: emd_36571.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of PLC gamma 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 216 pix.
= 237.6 Å		1.1 Å/pix.
x 216 pix.
= 237.6 Å		1.1 Å/pix.
x 216 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.7853274 - 2.9821913
Average (Standard dev.)0.0018947035 (±0.07528456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36571_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of PLC gamma 2

Fileemd_36571_half_map_1.map
AnnotationHalf map A of PLC gamma 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of PLC gamma 2

Fileemd_36571_half_map_2.map
AnnotationHalf map B of PLC gamma 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PLCg2 and FGFR1

EntireName: PLCg2 and FGFR1
Components
  • Complex: PLCg2 and FGFR1
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2

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Supramolecule #1: PLCg2 and FGFR1

SupramoleculeName: PLCg2 and FGFR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 147.8 KDa

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Macromolecule #1: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2

MacromoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphoinositide phospholipase C
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 148.074578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTTVNVDSL AEYEKSQIKR ALELGTVMTV FSFRKSTPER RTVQVIMETR QVAWSKTADK IEGFLDIMEI KEIRPGKNSK DFERAKAVR QKEDCCFTIL YGTQFVLSTL SLAADSKEDA VNWLSGLKIL HQEAMNASTP TIIESWLRKQ IYSVDQTRRN S ISLRELKT ...String:
MSTTVNVDSL AEYEKSQIKR ALELGTVMTV FSFRKSTPER RTVQVIMETR QVAWSKTADK IEGFLDIMEI KEIRPGKNSK DFERAKAVR QKEDCCFTIL YGTQFVLSTL SLAADSKEDA VNWLSGLKIL HQEAMNASTP TIIESWLRKQ IYSVDQTRRN S ISLRELKT ILPLINFKVS SAKFLKDKFV EIGAHKDELS FEQFHLFYKK LMFEQQKSIL DEFKKDSSVF ILGNTDRPDA SA VYLHDFQ RFLIHEQQEH WAQDLNKVRE RMTKFIDDTM RETAEPFLFV DEFLTYLFSR ENSIWDEKYD AVDMQDMNNP LSH YWISSS HNTYLTGDQL RSESSPEAYI RCLRMGCRCI ELDCWDGPDG KPVIYHGWTR TTKIKFDDVV QAIKDHAFVT SSFP VILSI EEHCSVEQQR HMAKAFKEVF GDLLLTKPTE ASADQLPSPS QLREKIIIKH KKLGPRGDVD VNMEDKKDEH KQQGE LYMW DSIDQKWTRH YCAIADAKLS FSDDIEQTME EEVPQDIPPT ELHFGEKWFH KKVEKRTSAE KLLQEYCMET GGKDGT FLV RESETFPNDY TLSFWRSGRV QHCRIRSTME GGTLKYYLTD NLTFSSIYAL IQHYRETHLR CAEFELRLTD PVPNPNP HE SKPWYYDSLS RGEAEDMLMR IPRDGAFLIR KREGSDSYAI TFRARGKVKH CRINRDGRHF VLGTSAYFES LVELVSYY E KHSLYRKMRL RYPVTPELLE RYNMERDINS LYDVSRMYVD PSEINPSMPQ RTVKALYDYK AKRSDELSFC RGALIHNVS KEPGGWWKGD YGTRIQQYFP SNYVEDISTA DFEELEKQII EDNPLGSLCR GILDLNTYNV VKAPQGKNQK SFVFILEPKQ QGDPPVEFA TDRVEELFEW FQSIREITWK IDTKENNMKY WEKNQSIAIE LSDLVVYCKP TSKTKDNLEN PDFREIRSFV E TKADSIIR QKPVDLLKYN QKGLTRVYPK GQRVDSSNYD PFRLWLCGSQ MVALNFQTAD KYMQMNHALF SLNGRTGYVL QP ESMRTEK YDPMPPESQR KILMTLTVKV LGARHLPKLG RSIACPFVEV EICGAEYDNN KFKTTVVNDN GLSPIWAPTQ EKV TFEIYD PNLAFLRFVV YEEDMFSDPN FLAHATYPIK AVKSGFRSVP LKNGYSEDIE LASLLVFCEM RPVLESEEEL YSSC RQLRR RQEELNNQLF LYDTHQNLRN ANRDALVKEF SVNENQLQLY QEKCNKRLRE KRVSNSKFYS

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.7 mg/mL
BufferpH: 7.9 / Details: 25 mM Tris pH 7.9, 150 mM NaCl, 1mM TCEP
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0932 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189652
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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