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- PDB-9qb7: Structure of rat Phospholipase C gamma 1 mutant S345F -

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Basic information

Entry
Database: PDB / ID: 9qb7
TitleStructure of rat Phospholipase C gamma 1 mutant S345F
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / HYDROLASE COMPLEX AUTOINHIBITED STATE / MUTANT / S345F
Function / homology
Function and homology information


PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / ISG15 antiviral mechanism ...PECAM1 interactions / EGFR interacts with phospholipase C-gamma / Activated NTRK2 signals through PLCG1 / Activated NTRK3 signals through PLCG1 / phosphatidylinositol catabolic process / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Phospholipase C-mediated cascade; FGFR2 / ISG15 antiviral mechanism / Downstream signal transduction / Signaling by ALK / Generation of second messenger molecules / Role of phospholipids in phagocytosis / DAP12 signaling / FCERI mediated Ca+2 mobilization / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / inositol trisphosphate biosynthetic process / RET signaling / Synthesis of IP3 and IP4 in the cytosol / inositol trisphosphate metabolic process / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / phosphatidylinositol metabolic process / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / phosphatidylinositol-mediated signaling / response to gravity / positive regulation of epithelial cell migration / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / ruffle / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / guanyl-nucleotide exchange factor activity / positive regulation of release of sequestered calcium ion into cytosol / insulin receptor binding / cell projection / phosphoprotein binding / response to hydrogen peroxide / calcium-mediated signaling / receptor tyrosine kinase binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / ruffle membrane / epidermal growth factor receptor signaling pathway / positive regulation of angiogenesis / cell-cell junction / calcium ion transport / cell migration / T cell receptor signaling pathway / lamellipodium / in utero embryonic development / calcium ion binding / protein kinase binding / glutamatergic synapse / plasma membrane / cytoplasm / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y domain / Phosphatidylinositol-specific phospholipase C, Y domain ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / PLCG EF-hand motif 2 / 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. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / 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 / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsPinotsis, N. / Katan, M. / Lalovic, D. / Gregory, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.J. / Year: 2025
Title: Characterisation of an allosteric site in PLC gamma enzymes and implications for development of their specific inhibitors.
Authors: Bunney, T.D. / Nyvall, H.G. / Macrae, C. / Lalovic, D. / Gregory, A. / Le Huray, K.I.P. / Harvey, N. / Pinotsis, N. / Kalli, A.C. / Waudby, C.A. / Burke, J.E. / Katan, M.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3812
Polymers146,2851
Non-polymers961
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area51410 Å2
Unit cell
Length a, b, c (Å)72.442, 82.391, 230.676
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / Phosphoinositide phospholipase C-gamma-1 / Phospholipase C-gamma-1 / PLC-gamma-1


Mass: 146285.031 Da / Num. of mol.: 1 / Mutation: S345F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P10686, phosphoinositide phospholipase C
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 18.7 % PEG 3350, 0.1 M CBTP, PH 7.0 / PH range: 6.8 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953738 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 13, 2023
RadiationMonochromator: CRL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953738 Å / Relative weight: 1
ReflectionResolution: 2.56→115.338 Å / Num. obs: 547294 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 49.77 Å2 / CC1/2: 0.987 / Net I/σ(I): 8.5
Reflection shellResolution: 2.56→2.605 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 26960 / CC1/2: 0.342 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→41.2 Å / SU ML: 0.3369 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.3681
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2333 2289 5.06 %
Rwork0.1881 42904 -
obs0.1904 45193 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.4 Å2
Refinement stepCycle: LAST / Resolution: 2.56→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9062 0 5 322 9389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00859299
X-RAY DIFFRACTIONf_angle_d1.045412579
X-RAY DIFFRACTIONf_chiral_restr0.05711338
X-RAY DIFFRACTIONf_plane_restr0.00851634
X-RAY DIFFRACTIONf_dihedral_angle_d6.94891223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.620.33191250.29012540X-RAY DIFFRACTION96.04
2.62-2.680.33741480.27362632X-RAY DIFFRACTION98.86
2.68-2.740.30281350.25462656X-RAY DIFFRACTION99.71
2.74-2.820.29461510.23362631X-RAY DIFFRACTION99.93
2.82-2.90.3031490.24652663X-RAY DIFFRACTION100
2.9-30.31270.24982641X-RAY DIFFRACTION100
3-3.10.31281340.25342670X-RAY DIFFRACTION100
3.1-3.230.28551270.23262691X-RAY DIFFRACTION100
3.23-3.370.271390.20852666X-RAY DIFFRACTION100
3.37-3.550.2491310.19772707X-RAY DIFFRACTION99.96
3.55-3.770.26061500.18952674X-RAY DIFFRACTION99.89
3.77-4.060.22031290.16582720X-RAY DIFFRACTION99.93
4.06-4.470.16571620.13562675X-RAY DIFFRACTION99.89
4.47-5.120.17151610.13522707X-RAY DIFFRACTION99.9
5.12-6.450.2091550.17142759X-RAY DIFFRACTION99.97
6.45-41.20.20891660.16762872X-RAY DIFFRACTION99.67
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7154430458480.150801370212-0.4579665387151.243836405770.491648241020.5382880703260.08220074676380.651135266375-0.128920850650.139976260622-0.1397448657380.2632663904190.29933056188-1.109619456550.1353857667820.283456999549-0.230720874192-0.01456947039341.19572228737-0.02030145067440.484140929447-44.490749212510.1069793389-46.0022402982
20.691222189614-0.419420531902-0.145183018680.4900670414310.07925505162660.9953442075040.0435910614025-0.01859020260840.19072223660.3061506619890.03260042696780.46909141287-0.192643636344-0.5116766664440.0003301644405870.4414759980310.1370125648030.1016834908410.6274579166620.1396385992370.587027145874-46.501406504432.3519230372-23.0930739567
30.3354470718720.077502270042-0.4230200659850.681464962640.01787519847021.02100350993-0.06157500135820.1621306296710.00428256850758-0.1553465063830.09739922091160.04099515539260.105780387833-0.270682148982-4.65138967492E-50.347965950839-0.0243428460633-0.02386124363350.4110031033570.04723398771980.322237478522-16.070740331617.9321102588-55.0618808013
40.245929849055-0.2906374730890.117551245210.474628590840.235337466380.5727150341510.0410448270774-0.009357105241950.01385414427870.03048507236230.0769239493976-0.0328194423613-0.0355629467408-0.130133192546-0.0002787003566110.3971518059190.0273808376980.04206379294620.3310800105850.06319947661610.377274483266-7.34113743817-4.42170232056-34.2854241414
50.9631317878450.1778275353180.7957879182950.707868816499-0.3373977095390.994545205530.0185645654695-0.0001782540842250.0490005732142-0.0553557817330.022362475609-0.0310400763240.03443411977160.0498913256038-0.0001615140917220.426458193770.002608866685860.02796309787640.3831844141720.02255274208950.388957910243-57.3227944027-14.8747084901-6.72738455345
60.21659371205-0.187698701138-0.2574888589820.561537134783-0.09802874916120.6806558625940.08936950554160.1208046177030.05265328725810.0106041002272-0.04607334867670.019753933264-0.0924461033561-0.0377605226233.54049282897E-50.3706729625580.02447295942240.05884700285290.2842012868930.05292702882580.329469355488-26.1451244731-3.46281229429-9.27951601485
70.5804884905970.1207993514120.2341753578290.3173617574090.1280109245770.3168309097330.07414762796620.130520928832-0.06959097445250.0105673281387-0.0690752887485-0.160034271357-0.03794396965440.08764086041580.0001607286845260.4295475389950.0466122361025-0.03140265401050.3358108051140.02451847244030.392390423566-5.21686835522-32.8922792187-16.2032572596
80.597837484916-0.278476322609-0.04845198204480.4380183726550.05351229982760.4596337759350.015476448660.0491395166946-0.08902834614710.008748472893950.06166314496440.04909087694110.1632975777870.01930303298389.56639546638E-50.404746134934-0.0224889789635-0.00145620736280.377987665460.005642695483070.333486625547-3.31818341203-11.4074821598-32.0875386185
90.122145591922-0.183382545268-0.1623865044190.7879543923810.01907106916221.03755312381-0.00874656009434-0.0741861777482-0.005039409196670.02816263810660.0564437592073-0.155630761217-0.073556901290.006387639475715.8877571439E-50.298585293216-0.006264585651820.007400027675810.3420563705820.04300636334760.390789239107-6.2231587663226.3505011154-45.1224959607
100.6115686441-0.14671254465-0.1177376587310.507816662536-0.02118995549540.450992601323-0.0523335259655-0.0147584837929-0.02805286401610.2598118938830.113021739155-0.00311071655954-0.0955380894245-0.03755212756053.1873989491E-60.4016964356880.03683804653550.03063354672410.3322900632790.0576858965860.358651019165-24.30892773729.7805158482-22.7412672541
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and ((resseq 19:148))19 - 1481 - 130
22chain 'A' and ((resseq 149:308))149 - 308131 - 263
33chain 'A' and ((resseq 309:478))309 - 478264 - 433
44chain 'A' and ((resseq 479:524))479 - 524434 - 479
55chain 'A' and ((resseq 545:661))545 - 661480 - 596
66chain 'A' and ((resseq 662:765))662 - 765597 - 700
77chain 'A' and ((resseq 766:851))766 - 851701 - 764
88chain 'A' and ((resseq 852:934))852 - 934765 - 847
99chain 'A' and ((resseq 947:1084))947 - 1084848 - 985
1010chain 'A' and ((resseq 1085:1215))1085 - 1215986 - 1116

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