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- EMDB-28268: Phospholipase C beta 3 (PLCb3) in complex with Gbg on lipid nanodiscs -

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Basic information

Entry
Database: EMDB / ID: EMD-28268
TitlePhospholipase C beta 3 (PLCb3) in complex with Gbg on lipid nanodiscs
Map datafinal sharpened map
Sample
  • Complex: Phospholipase C beta 3 (PLCb3) in complex with two copies of Gbg on lipid nanodiscs.
    • Complex: Phospholipase C beta 3 (PLCb3)
      • Protein or peptide: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
    • Complex: G protein beta subunit (Gb1)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: G protein gamma subunit 2 (Gg2)
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: G protein beta subunit (Gb1)
    • Complex: 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: 3.3 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-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28268.png

Downloads & links

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Map

FileDownload / File: emd_28268.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å		0.84 Å/pix.
x 384 pix.
= 324.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.362
Minimum - Maximum-1.8438052 - 3.5987947
Average (Standard dev.)0.0029726913 (±0.077773996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 324.096 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: final unsharpened map

Fileemd_28268_additional_1.map
Annotationfinal unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28268_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28268_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Phospholipase C beta 3 (PLCb3) in complex with two copies of Gbg ...

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

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Supramolecule #1: Phospholipase C beta 3 (PLCb3) in complex with two copies of Gbg ...

SupramoleculeName: Phospholipase C beta 3 (PLCb3) in complex with two copies of Gbg on lipid nanodiscs.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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)

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Supramolecule #3: G protein beta subunit (Gb1)

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

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

SupramoleculeName: 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: G protein beta subunit (Gb1)

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

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

SupramoleculeName: G protein gamma subunit 2 (Gg2) / type: complex / ID: 6 / Parent: 1
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: 139.055625 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPSRASTMHA LQLEPPTVVE TLRRGSKFIK WDEETSSRNL VTLRVDPNGF FLYWTGPNME VDTLDISSIR DTRTGRYARL PKDPKIREV LGFGGPDARL EEKLMTVVSG PDPVNTVFLN FMAVQDDTAK VWSEELFKLA MNILAQNASR NTFLRKAYTK L KLQVNQDG ...String:
GPSRASTMHA LQLEPPTVVE TLRRGSKFIK WDEETSSRNL VTLRVDPNGF FLYWTGPNME VDTLDISSIR DTRTGRYARL PKDPKIREV LGFGGPDARL EEKLMTVVSG PDPVNTVFLN FMAVQDDTAK VWSEELFKLA MNILAQNASR NTFLRKAYTK L KLQVNQDG RIPVKNILKM FSADKKRVET ALESCGLKFN RSESIRPDEF SLEIFERFLN KLCLRPDIDK ILLEIGAKGK PY LTLEQLM DFINQKQRDP RLNEVLYPPL RPSQARLLIE KYEPNQQFLE RDQMSMEGFS RYLGGEENGI LPLEALDLST DMT QPLSAY FINSSHNTYL TAGQLAGTSS VEMYRQALLW GCRCVELDVW KGRPPEEEPF ITHGFTMTTE VPLRDVLEAI AETA FKTSP YPVILSFENH VDSAKQQAKM AEYCRSIFGD ALLIEPLDKY PLAPGVPLPS PQDLMGRILV KNKKRHRPSA GGPDS AGRK RPLEQSNSAL SESSAATEPS SPQLGSPSSD SCPGLSNGEE VGLEKPSLEP QKSLGDEGLN RGPYVLGPAD REDEEE DEE EEEQTDPKKP TTDEGTASSE VNATEEMSTL VNYIEPVKFK SFEAARKRNK CFEMSSFVET KAMEQLTKSP MEFVEYN KQ QLSRIYPKGT RVDSSNYMPQ LFWNVGCQLV ALNFQTLDVA MQLNAGVFEY NGRSGYLLKP EFMRRPDKSF DPFTEVIV D GIVANALRVK VISGQFLSDR KVGIYVEVDM FGLPVDTRRK YRTRTSQGNS FNPVWDEEPF DFPKVVLPTL ASLRIAAFE EGGKFVGHRI LPVSAIRSGY HYVCLRNEAN QPLCLPALLI YTEASDYIPD DHQDYAEALI NPIKHVSLMD QRARQLAALI GESEAQAGQ ETCQDTQSQQ LGSQPSSNPT PSPLDASPRR PPGPTTSPAS TSLSSPGQRD DLIASILSEV APTPLDELRG H KALVKLRS RQERDLRELR KKHQRKAVTL TRRLLDGLAQ AQAEGRCRLR PGALGGAADV EDTKEGEDEA KRYQEFQNRQ VQ SLLELRE AQVDAEAQRR LEHLRQALQR LREVVLDANT TQFKRLKEMN EREKKELQKI LDRKRHNSIS EAKMRDKHKK EAE LTEINR RHITESVNSI RRLEEAQKQR HDRLVAGQQQ VLQQLAEEEP KLLAQLAQEC QEQRARLPQE IRRSLLGEMP EGLG DGPLV ACASNGHAPG SSGHLSGADS ESQEENTQL

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 69.14 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3993932
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53984
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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