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- EMDB-36573: Cryo EM map of full length PLC gamma 2 and FGFR1 Kinase Domain -

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Entry
Database: EMDB / ID: EMD-36573
TitleCryo EM map of full length PLC gamma 2 and FGFR1 Kinase Domain
Map dataEM map of PLC gamma 2 and FGFR1K complex
Sample
  • Complex: PLCg2 and FGFR1
    • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
    • Protein or peptide: Fibroblast growth factor receptor 1
KeywordsPLCg2 / PLC gamma 2 / HYDROLASE
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 / phosphoinositide phospholipase C / regulation of phosphate transport / FGFR1c and Klotho ligand binding and activation / regulation of lateral mesodermal cell fate specification / antifungal innate immune response / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / vitamin D3 metabolic process / cementum mineralization / positive regulation of interleukin-23 production / cellular response to lectin / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / response to sodium phosphate / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / receptor-receptor interaction / Epithelial-Mesenchymal Transition (EMT) during gastrulation / phosphorylation-dependent protein binding / positive regulation of phospholipase activity / chordate embryonic development / positive regulation of cell cycle G1/S phase transition / phosphatidylinositol metabolic process / Toll Like Receptor 4 (TLR4) Cascade / response to yeast / positive regulation of parathyroid hormone secretion / auditory receptor cell development / mesenchymal cell proliferation / paraxial mesoderm development / positive regulation of phagocytosis, engulfment / cell activation / positive regulation of neuroinflammatory response / FGFR1b ligand binding and activation / regulation of postsynaptic density assembly / Signaling by activated point mutants of FGFR1 / Erythropoietin activates Phospholipase C gamma (PLCG) / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / phospholipase C activity / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / lung-associated mesenchyme development / phosphatidylinositol biosynthetic process / cell projection assembly / programmed cell death / macrophage activation involved in immune response / phospholipid catabolic process / outer ear morphogenesis / cellular response to lipid / embryonic limb morphogenesis / regulation of canonical NF-kappaB signal transduction / positive regulation of endothelial cell chemotaxis / negative regulation of programmed cell death / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / ureteric bud development / positive regulation of macrophage cytokine production / middle ear morphogenesis / skeletal system morphogenesis / inner ear morphogenesis / toll-like receptor signaling pathway / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / Dectin-2 family / midbrain development / positive regulation of NLRP3 inflammasome complex assembly / Fc-epsilon receptor signaling pathway / intracellular vesicle / Synthesis of IP3 and IP4 in the cytosol / stimulatory C-type lectin receptor signaling pathway / fibroblast growth factor binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of MAP kinase activity / B cell activation / regulation of cell differentiation / positive regulation of intracellular signal transduction / 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 / epithelial to mesenchymal transition / fibroblast growth factor receptor signaling pathway / positive regulation of blood vessel endothelial cell migration / positive regulation of type I interferon production / 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 ...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 / 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. / PH-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_36573.png

Downloads & links

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Map

FileDownload / File: emd_36573.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map of PLC gamma 2 and FGFR1K complex
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-0.8894118 - 1.8723263
Average (Standard dev.)0.0024268182 (±0.06400126)
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_36573_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 and FGFR1K complex

Fileemd_36573_half_map_1.map
AnnotationHalf map A of PLC gamma 2 and FGFR1K complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B pf PLC gamma 2 and FGFR1K complex

Fileemd_36573_half_map_2.map
AnnotationHalf map B pf PLC gamma 2 and FGFR1K complex
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
    • Protein or peptide: Fibroblast growth factor receptor 1

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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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Macromolecule #2: Fibroblast growth factor receptor 1

MacromoleculeName: Fibroblast growth factor receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.97868 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSWKCLLFW AVLVTATLCT ARPSPTLPEQ AQPWGAPVEV ESFLVHPGDL LQLRCRLRDD VQSINWLRDG VQLAESNRTR ITGEEVEVQ DSVPADSGLY ACVTSSPSGS DTTYFSVNVS DALPSSEDDD DDDDSSSEEK ETDNTKPNRM PVAPYWTSPE K MEKKLHAV ...String:
MWSWKCLLFW AVLVTATLCT ARPSPTLPEQ AQPWGAPVEV ESFLVHPGDL LQLRCRLRDD VQSINWLRDG VQLAESNRTR ITGEEVEVQ DSVPADSGLY ACVTSSPSGS DTTYFSVNVS DALPSSEDDD DDDDSSSEEK ETDNTKPNRM PVAPYWTSPE K MEKKLHAV PAAKTVKFKC PSSGTPNPTL RWLKNGKEFK PDHRIGGYKV RYATWSIIMD SVVPSDKGNY TCIVENEYGS IN HTYQLDV VERSPHRPIL QAGLPANKTV ALGSNVEFMC KVYSDPQPHI QWLKHIEVNG SKIGPDNLPY VQILKTAGVN TTD KEMEVL HLRNVSFEDA GEYTCLAGNS IGLSHHSAWL TVLEALEERP AVMTSPLYLE IIIYCTGAFL ISCMVGSVIV YKMK SGTKK SDFHSQMAVH KLAKSIPLRR QVTVSADSSA SMNSGVLLVR PSRLSSSGTP MLAGVSEYEL PEDPRWELPR DRLVL GKPL GEGCFGQVVL AEAIGLDKDK PNRVTKVAVK MLKSDATEKD LSDLISEMEM MKMIGKHKNI INLLGACTQD GPLYVI VEY ASKGNLREYL QARRPPGLEY CYNPSHNPEE QLSSKDLVSC AYQVARGMEY LASKKCIHRD LAARNVLVTE DNVMKIA DF GLARDIHHID YYKKTTNGRL PVKWMAPEAL FDRIYTHQSD VWSFGVLLWE IFTLGGSPYP GVPVEELFKL LKEGHRMD K PSNCTNELYM MMRDCWHAVP SQRPTFKQLV EDLDRIVALT SNQEYLDLSM PLDQYSPSFP DTRSSTCSSG EDSVFSHEP LPEEPCLPRH PAQLANGGLK RR

UniProtKB: Fibroblast growth factor receptor 1

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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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45439
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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