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- EMDB-43927: Cryo-EM structure of Phospholipase C epsilon PH-C terminus in com... -

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Entry
Database: EMDB / ID: EMD-43927
TitleCryo-EM structure of Phospholipase C epsilon PH-C terminus in complex with RhoA-GTP
Map data
Sample
  • Complex: PLCe PH-C in complex with RhoA-GTP
    • Complex: PH-C fragment (837-2281) of PLC epsilon
      • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
    • Complex: RhoA-GTP
      • Protein or peptide: Transforming protein RhoA
  • Ligand: CALCIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsGPCR signaling / complex / phospholipase / PIP2 hydrolysis / G protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration ...diacylglycerol biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / phosphoinositide phospholipase C / alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / phosphatidylinositol metabolic process / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / phospholipase C activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / glomerulus development / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / phosphatidylinositol-mediated signaling / myosin binding / regulation of neuron projection development / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / lipid catabolic process / positive regulation of lamellipodium assembly / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / release of sequestered calcium ion into cytosol / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / guanyl-nucleotide exchange factor activity / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development
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 / Small GTPase Rho / small GTPase Rho family profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / EF-hand domain pair / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transforming protein RhoA / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOhri V / Lyon AM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)1R01HL141076-01 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Phospholipase C epsilon PH-C terminus in complex with RhoA-GTP
Authors: Ohri V / Lyon AM
History
DepositionMar 5, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43927.png

Downloads & links

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Map

FileDownload / File: emd_43927.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 512 pix.
= 269.824 Å		0.53 Å/pix.
x 512 pix.
= 269.824 Å		0.53 Å/pix.
x 512 pix.
= 269.824 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.527 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.31626254 - 0.47283724
Average (Standard dev.)0.00035438413 (±0.008634226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 269.824 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43927_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43927_half_map_1.map
Projections & Slices
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Slices (1/2)
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Histogram (log scale)

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Half map: #1

Fileemd_43927_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : PLCe PH-C in complex with RhoA-GTP

EntireName: PLCe PH-C in complex with RhoA-GTP
Components
  • Complex: PLCe PH-C in complex with RhoA-GTP
    • Complex: PH-C fragment (837-2281) of PLC epsilon
      • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
    • Complex: RhoA-GTP
      • Protein or peptide: Transforming protein RhoA
  • Ligand: CALCIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: PLCe PH-C in complex with RhoA-GTP

SupramoleculeName: PLCe PH-C in complex with RhoA-GTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 24 KDa

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Supramolecule #2: PH-C fragment (837-2281) of PLC epsilon

SupramoleculeName: PH-C fragment (837-2281) of PLC epsilon / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: RhoA-GTP

SupramoleculeName: RhoA-GTP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1

MacromoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphoinositide phospholipase C
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 165.182938 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHSSGV DLGTENLYFQ SNADHGTELI PWYVLSIQAD VHQFLLQGAT VIHYDQDTHL SARCFLQLQP DNSTLTWMKP PTASPAGAR LKLGVLSNVA EPGKFPSLGN AGVSGLVEGI LDLFSVKAVY MGHPGIDIHT VCVQNKLSSM LLSETGVTLL Y GLQTTDNR ...String:
HHHHHHSSGV DLGTENLYFQ SNADHGTELI PWYVLSIQAD VHQFLLQGAT VIHYDQDTHL SARCFLQLQP DNSTLTWMKP PTASPAGAR LKLGVLSNVA EPGKFPSLGN AGVSGLVEGI LDLFSVKAVY MGHPGIDIHT VCVQNKLSSM LLSETGVTLL Y GLQTTDNR LLHFVAPKHT AKMLFSGLLE LTTAVRKIRK FPDQRQQWLR KQYVSFYQED GRYEGPTLAH AVELFGGRRW ST RNPSPGM SAKNAEKPNM QRNNTLGIST TKKKKKMLMR GESGEVTDDE MATRKAKMYR ECRSRSGSDP QEANEQEDSE ANV ITNPPN PLHSRRAYSL TTAGSPNLAT GMSSPISAWS SSSWHGRIKG GMKGFQSFMV SDSNMSFIEF VELFKSFSIR SRKD LKDIF DIYSVPCNRS ASESTPLYTN LTIEENTNDL QPDLDLLTRN VSDLGLFMKS KQQLSDNQRQ ISDAIAAASI VTNGT GIES TSLGIFGVGI LQLNDFLVNC QGEHCTYDEI LSIIQKFEPN ISMCHQGLLS FEGFARFLMD KDNFASKNDE SRENKK DLQ LPLSYYYIES SHNTYLTGHQ LKGESSVELY SQVLLQGCRS IELDCWDGDD GMPIIYHGHT LTTKIPFKEV VEAIDRS AF ITSDLPIIIS IENHCSLPQQ RKMAEIFKSV FGEKLVAKFL FETDFSDDPM LPSPDQLRRK VLLKNKKLKA HQTPVDIL K QKAHQLASMQ TQAFTGGNAN PPPASNEEEE DEEDEYDYDY ESLSDDNILE DRPENKSCAD KLQFEYNEEV PKRIKKADN SSGNKGKVYD MELGEEFYLP QNKKESRQIA PELSDLVIYC QAVKFPGLST LNSSGSGRGK ERKSRKSIFG NNPGRMSPGE TASFNRTSG KSSCEGIRQI WEEPPLSPNT SLSAIIRTPK CYHISSLNEN AAKRLCRRYS QKLIQHTACQ LLRTYPAATR I DSSNPNPL MFWLHGIQLV ALNYQTDDLP LHLNAAMFEA NGGCGYVLKP PVLWDKSCPM YQKFSPLERD LDAMDPATYS LT IISGQNV CPSNSTGSPC IEVDVLGMPL DSCHFRTKPI HRNTLNPMWN EQFLFRVHFE DLVFLRFAVV ENNSSAITAQ RII PLKALK RGYRHLQLRN LHNEILEISS LFINSRRMED NPSGSTRPAS LMFNTEERKC SQTHKVTVHG VPGPEPFAVF TINE GTKAK QLLQQILAVD QDTKLTAADY FLMEEKHFIS KEKNECRKQP FQRAVGPEED IVQILNSWFP EEGYVGRIVL KPQQE TLEE KNIVHDDREV ILSSEEESFF VQVHDVSPEQ PRTVIKAPRV STAQDVIQQT LCKAKYSYSI LNNPNPCDYV LLEEVM KDA PNKKSSTPKS SQRILLDQEC VFQAQSKWKG AGKFILKLKE QVQASREDKR RGISFASELK KLTKSTKQTR GLTSPPQ LV ASESVQSKEE KPMGALASGD TAGYQS

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1

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Macromolecule #2: Transforming protein RhoA

MacromoleculeName: Transforming protein RhoA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.569055 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHDYDI PTTENLYFQG AMDPAAIRKK LVIVGDGACG KTCLLIVFSK DQFPEVYVPT VFENYVADIE VDGKQVELAL WDTAGQEDY DRLRPLSYPD TDVILMCFSI DSPDSLENIP EKWTPEVKHF CPNVPIILVG NKKDLRNDEH TRRELAKMKQ E PVKPEEGR ...String:
HHHHHHDYDI PTTENLYFQG AMDPAAIRKK LVIVGDGACG KTCLLIVFSK DQFPEVYVPT VFENYVADIE VDGKQVELAL WDTAGQEDY DRLRPLSYPD TDVILMCFSI DSPDSLENIP EKWTPEVKHF CPNVPIILVG NKKDLRNDEH TRRELAKMKQ E PVKPEEGR DMANRIGAFG YMECSAKTKD GVREVFEMAT RAALQARRGK KKSGCLVL

UniProtKB: Transforming protein RhoA

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClsodium chloride
2.0 mMDTTdithiothreitol
0.1 mMEDTAethylenediaminetetraacetic acid
0.1 mMEGTAegtazic acid
1.0 mMMgCl2magnesium dichloride
0.04 mMGTPguanosine triphosphate
0.5 mMCaCl2calcium chloride
2.5 mMCHAPS3-((3-cholamidopropyl) dimethylammonio)-1-propanesulfonate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6345 / Average exposure time: 3.2 sec. / Average electron dose: 57.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1329298
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 209463
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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