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- EMDB-28267: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes -

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Basic information

Entry
Database: EMDB / ID: EMD-28267
TitlePhospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
Map datafinal sharpened map
Sample
  • Complex: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
    • Complex: phospholipase C beta 3 (PLCb3)
      • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
    • Complex: human G protein beta subunit 1 (Gb1)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: bovine G protein gamma subunit 2 (Gg2)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: human G protein beta subunit 1 (Gb1)
    • Complex: bovine G protein gamma subunit 2 (Gg2)
  • Ligand: CALCIUM ION
KeywordsPIP2 degradation / IP3 production / DAG production / G protein signaling / HYDROLASE
Function / homology
Function and homology information


phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phosphatidylinositol metabolic process / PLC beta mediated events / regulation of systemic arterial blood pressure / phospholipase C activity / phosphatidylinositol phospholipase C activity / postsynaptic cytosol / Synthesis of IP3 and IP4 in the cytosol ...phosphoinositide phospholipase C / Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion / Acetylcholine regulates insulin secretion / phosphatidylinositol metabolic process / PLC beta mediated events / regulation of systemic arterial blood pressure / phospholipase C activity / phosphatidylinositol phospholipase C activity / postsynaptic cytosol / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol-mediated signaling / lipid catabolic process / release of sequestered calcium ion into cytosol / molecular function activator activity / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / fibroblast proliferation / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / molecular adaptor activity / calmodulin binding / cadherin binding / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / calcium ion binding / synapse / protein-containing complex binding / signal transduction / protein-containing complex / extracellular exosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain ...Phospholipase C-beta, C-terminal domain / PLC-beta C terminal / PLC-beta, PH domain / Phospholipase C-beta, C-terminal domain superfamily / : / PH domain / Phosphoinositide phospholipase C beta1-4-like EF-hand domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase beta / 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 / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / EF-hand domain pair / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFalzone ME / MacKinnon R
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM142137 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: activates hydrolysis by recruiting and orienting on the membrane surface.
Authors: Maria E Falzone / Roderick MacKinnon /
Abstract: catalyze the hydrolysis of phosphatidylinositol 4, 5-bisphosphate [Formula: see text] into [Formula: see text] [Formula: see text] and [Formula: see text]  [Formula: see text]. [Formula: see text] ... catalyze the hydrolysis of phosphatidylinositol 4, 5-bisphosphate [Formula: see text] into [Formula: see text] [Formula: see text] and [Formula: see text]  [Formula: see text]. [Formula: see text] regulates the activity of many membrane proteins, while and lead to increased intracellular Ca levels and activate protein kinase C, respectively. are regulated by G protein-coupled receptors through direct interaction with [Formula: see text] and [Formula: see text] and are aqueous-soluble enzymes that must bind to the cell membrane to act on their lipid substrate. This study addresses the mechanism by which [Formula: see text] activates 3. We show that 3 functions as a slow Michaelis-Menten enzyme ( [Formula: see text] ) on membrane surfaces. We used membrane partitioning experiments to study the solution-membrane localization equilibrium of 3. Its partition coefficient is such that only a small quantity of 3 exists in the membrane in the absence of [Formula: see text] . When [Formula: see text] is present, equilibrium binding on the membrane surface increases 3 in the membrane, increasing [Formula: see text] in proportion. Atomic structures on membrane vesicle surfaces show that two [Formula: see text] anchor 3 with its catalytic site oriented toward the membrane surface. Taken together, the enzyme kinetic, membrane partitioning, and structural data show that [Formula: see text] activates by increasing its concentration on the membrane surface and orienting its catalytic core to engage [Formula: see text] . This principle of activation explains rapid stimulated catalysis with low background activity, which is essential to the biological processes mediated by [Formula: see text], and .
History
DepositionSep 28, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateSep 25, 2024-
Current statusSep 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28267.png

Downloads & links

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Map

FileDownload / File: emd_28267.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfinal sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 344 pix.
= 288.616 Å		0.84 Å/pix.
x 344 pix.
= 288.616 Å		0.84 Å/pix.
x 344 pix.
= 288.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.7107834 - 1.0291244
Average (Standard dev.)0.002008854 (±0.026454423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 288.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: final unsharpened map

Fileemd_28267_additional_1.map
Annotationfinal unsharpened map
Projections & Slices
AxesZYX

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Additional map: reconstruction with membrane

Fileemd_28267_additional_2.map
Annotationreconstruction with membrane
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_28267_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_28267_half_map_2.map
Projections & Slices
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Sample components

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Entire : Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes

EntireName: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
Components
  • Complex: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
    • Complex: phospholipase C beta 3 (PLCb3)
      • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
    • Complex: human G protein beta subunit 1 (Gb1)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: bovine G protein gamma subunit 2 (Gg2)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: human G protein beta subunit 1 (Gb1)
    • Complex: bovine G protein gamma subunit 2 (Gg2)
  • Ligand: CALCIUM ION

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Supramolecule #1: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes

SupramoleculeName: Phospholipase C beta 3 (PLCb3) in complex with Gbg on liposomes
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: liposomes contain 2DOPE:1POPC:1POPS lipids
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 230 KDa

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Supramolecule #2: phospholipase C beta 3 (PLCb3)

SupramoleculeName: phospholipase C beta 3 (PLCb3) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 138 KDa

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Supramolecule #3: human G protein beta subunit 1 (Gb1)

SupramoleculeName: human G protein beta subunit 1 (Gb1) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: bovine G protein gamma subunit 2 (Gg2)

SupramoleculeName: bovine G protein gamma subunit 2 (Gg2) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: human G protein beta subunit 1 (Gb1)

SupramoleculeName: human G protein beta subunit 1 (Gb1) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: bovine G protein gamma subunit 2 (Gg2)

SupramoleculeName: bovine G protein gamma subunit 2 (Gg2) / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

MacromoleculeName: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
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: 138.830422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPSRATMALQ LEPPTVVETL RRGSKFIKWD EETSSRNLVT LRVDPNGFFL YWTGPNMEVD TLDISSIRDT RTGRYARLPK DPKIREVLG FGGPDARLEE KLMTVVSGPD PVNTVFLNFM AVQDDTAKVW SEELFKLAMN ILAQNASRNT FLRKAYTKLK L QVNQDGRI ...String:
GPSRATMALQ LEPPTVVETL RRGSKFIKWD EETSSRNLVT LRVDPNGFFL YWTGPNMEVD TLDISSIRDT RTGRYARLPK DPKIREVLG FGGPDARLEE KLMTVVSGPD PVNTVFLNFM AVQDDTAKVW SEELFKLAMN ILAQNASRNT FLRKAYTKLK L QVNQDGRI PVKNILKMFS ADKKRVETAL ESCGLKFNRS ESIRPDEFSL EIFERFLNKL CLRPDIDKIL LEIGAKGKPY LT LEQLMDF INQKQRDPRL NEVLYPPLRP SQARLLIEKY EPNQQFLERD QMSMEGFSRY LGGEENGILP LEALDLSTDM TQP LSAYFI NSSHNTYLTA GQLAGTSSVE MYRQALLWGC RCVELDVWKG RPPEEEPFIT HGFTMTTEVP LRDVLEAIAE TAFK TSPYP VILSFENHVD SAKQQAKMAE YCRSIFGDAL LIEPLDKYPL APGVPLPSPQ DLMGRILVKN KKRHRPSAGG PDSAG RKRP LEQSNSALSE SSAATEPSSP QLGSPSSDSC PGLSNGEEVG LEKPSLEPQK SLGDEGLNRG PYVLGPADRE DEEEDE EEE EQTDPKKPTT DEGTASSEVN ATEEMSTLVN YIEPVKFKSF EAARKRNKCF EMSSFVETKA MEQLTKSPME FVEYNKQ QL SRIYPKGTRV DSSNYMPQLF WNVGCQLVAL NFQTLDVAMQ LNAGVFEYNG RSGYLLKPEF MRRPDKSFDP FTEVIVDG I VANALRVKVI SGQFLSDRKV GIYVEVDMFG LPVDTRRKYR TRTSQGNSFN PVWDEEPFDF PKVVLPTLAS LRIAAFEEG GKFVGHRILP VSAIRSGYHY VCLRNEANQP LCLPALLIYT EASDYIPDDH QDYAEALINP IKHVSLMDQR ARQLAALIGE SEAQAGQET CQDTQSQQLG SQPSSNPTPS PLDASPRRPP GPTTSPASTS LSSPGQRDDL IASILSEVAP TPLDELRGHK A LVKLRSRQ ERDLRELRKK HQRKAVTLTR RLLDGLAQAQ AEGRCRLRPG ALGGAADVED TKEGEDEAKR YQEFQNRQVQ SL LELREAQ VDAEAQRRLE HLRQALQRLR EVVLDANTTQ FKRLKEMNER EKKELQKILD RKRHNSISEA KMRDKHKKEA ELT EINRRH ITESVNSIRR LEEAQKQRHD RLVAGQQQVL QQLAEEEPKL LAQLAQECQE QRARLPQEIR RSLLGEMPEG LGDG PLVAC ASNGHAPGSS GHLSGADSES QEENTQL

UniProtKB: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 37.41693 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.717917 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
GPMASNNTAS IAQARKLVEQ LKMEANIDRI KVSKAAADLM AYCEAHAKED PLLTPVPASE NPFREKKFFC

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 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

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 22 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsGbg was reconstituted at 1:15 (wt/wt). Final lipid concentration was 17.5 mM. PLCb3 concentration was 0.5 mg/mL

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 27454 / Average exposure time: 4.194 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1997424 / Details: trained model in crYOLO
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 121394
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 6 / Avg.num./class: 20000 / Software - Name: RELION
FSC plot (resolution estimation)

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