[English] 日本語
Yorodumi
- EMDB-43927: Cryo-EM structure of Phospholipase C epsilon PH-C terminus in com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / phosphatidylinositol metabolic process / negative regulation of intracellular steroid hormone receptor signaling pathway / 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 / cell junction assembly / regulation of modification of postsynaptic structure / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / apical junction assembly / glomerulus development / 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 oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / phosphatidylinositol-mediated signaling / androgen receptor signaling pathway / stress fiber assembly / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / skeletal muscle tissue development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / lipid catabolic process / GPVI-mediated activation cascade / positive regulation of lamellipodium assembly / Rho protein signal transduction / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / release of sequestered calcium ion into cytosol / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of cell migration / regulation of microtubule cytoskeleton organization / secretory granule membrane / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery
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 domain 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: Commun Biol / Year: 2025
Title: RhoA allosterically activates phospholipase Cε via its EF hands.
Authors: Vaani Ohri / Kadidia Samassekou / Kaushik Muralidharan / Elisabeth E Garland-Kuntz / Isaac J Fisher / William C Hogan / Bailey M Davis / Angeline M Lyon /
Abstract: Phospholipase Cε (PLCε) cleaves phosphatidylinositol lipids to increase intracellular Ca and activate protein kinase C (PKC) in response to stimulation of cell surface receptors. PLCε is activated ...Phospholipase Cε (PLCε) cleaves phosphatidylinositol lipids to increase intracellular Ca and activate protein kinase C (PKC) in response to stimulation of cell surface receptors. PLCε is activated via direct binding of small GTPases at the cytoplasmic leaflets of cellular membranes. In the cardiovascular system, the RhoA GTPase regulates PLCε to initiate a pathway that protects against ischemia/reperfusion injuries, but the underlying molecular mechanism is not known. We present here the cryo-electron microscopy (cryo-EM) reconstruction of RhoA bound to PLCε, showing that the G protein binds a unique insertion within the PLCε EF hands. Deletion of or mutations to this PLCε insertion decrease RhoA-dependent activation without impacting its regulation by other G proteins. Together, our data support a model wherein RhoA binding to PLCε allosterically activates the lipase and increases its interactions with the membrane, resulting in maximum activity and cardiomyocyte survival.
History
DepositionMar 5, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43927.png

Downloads & links

-
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)

Slices (1/2)

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 °

-
Supplemental data

-
Mask #1

Fileemd_43927_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_43927_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43927_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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

-
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)

-
Supramolecule #3: RhoA-GTP

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

-
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

-
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

-
Macromolecule #3: CALCIUM ION

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

-
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

-
Macromolecule #5: MAGNESIUM ION

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
Image processing

Particle selectionNumber selected: 1329298
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
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)

+
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