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- PDB-7z3j: Structure of crystallisable rat Phospholipase C gamma 1 in comple... -

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Basic information

Entry
Database: PDB / ID: 7z3j
TitleStructure of crystallisable rat Phospholipase C gamma 1 in complex with inositol 1,4,5-trisphosphate
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / HYDROLASE COMPLEX AUTOINHIBITED STATE
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 / response to curcumin / inositol trisphosphate metabolic process / phosphoinositide phospholipase C / FCERI mediated MAPK activation / response to gravity / 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 / 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 / positive regulation of release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / cell projection / phosphoprotein binding / insulin receptor binding / modulation of chemical synaptic transmission / calcium-mediated signaling / Schaffer collateral - CA1 synapse / receptor tyrosine kinase binding / response to hydrogen peroxide / epidermal growth factor receptor signaling pathway / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / calcium ion binding / protein kinase binding / glutamatergic synapse / plasma membrane / cytosol / cytoplasm
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 / Phosphatidylinositol-specific phospholipase Y-box domain profile. ...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 / SH2 domain superfamily / Src homology 3 domains / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / PH-like domain superfamily
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPinotsis, N. / Bunney, T.D. / Katan, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private560655 United Kingdom
CitationJournal: Sci Adv / Year: 2022
Title: Characterization of the membrane interactions of phospholipase C gamma reveals key features of the active enzyme.
Authors: Le Huray, K.I.P. / Bunney, T.D. / Pinotsis, N. / Kalli, A.C. / Katan, M.
History
DepositionMar 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)136,7677
Polymers135,9911
Non-polymers7776
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-26 kcal/mol
Surface area51770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.760, 82.440, 230.110
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: 135990.938 Da / Num. of mol.: 1
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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 %
Description: ugly small crystals, however they diffract well
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 18.7 % PEG 3350, 0.1 M CBTP / PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2→115.1 Å / Num. obs: 93254 / % possible obs: 98.8 % / Redundancy: 13.5 % / Biso Wilson estimate: 49.37 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.076 / Net I/σ(I): 10.83
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 28825 / CC1/2: 0.234

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSdata reduction
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bpc

6bpc


Resolution: 2→49.29 Å / SU ML: 0.3692 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.0714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2564 4642 5 %
Rwork0.2237 88273 -
obs0.2254 92915 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.64 Å2
Refinement stepCycle: LAST / Resolution: 2→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9063 0 44 243 9350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00879372
X-RAY DIFFRACTIONf_angle_d1.005712688
X-RAY DIFFRACTIONf_chiral_restr0.05521352
X-RAY DIFFRACTIONf_plane_restr0.0081646
X-RAY DIFFRACTIONf_dihedral_angle_d14.17263517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.46571480.43512803X-RAY DIFFRACTION94.8
2.02-2.050.43361510.41272853X-RAY DIFFRACTION97.37
2.05-2.070.40391500.38592924X-RAY DIFFRACTION98.84
2.07-2.10.35081530.3742899X-RAY DIFFRACTION98.99
2.1-2.130.37011530.35232938X-RAY DIFFRACTION99.01
2.13-2.150.40451540.35272907X-RAY DIFFRACTION99.16
2.15-2.190.39831540.33322947X-RAY DIFFRACTION99.01
2.19-2.220.36831540.31672927X-RAY DIFFRACTION99.16
2.22-2.250.36081530.31412907X-RAY DIFFRACTION98.87
2.25-2.290.32341520.31092889X-RAY DIFFRACTION96.54
2.29-2.330.38091530.30352924X-RAY DIFFRACTION99.55
2.33-2.370.30911540.29092931X-RAY DIFFRACTION99.64
2.37-2.420.33611560.28012965X-RAY DIFFRACTION99.33
2.42-2.470.33081550.27622933X-RAY DIFFRACTION99.1
2.47-2.520.32771570.26352974X-RAY DIFFRACTION99.68
2.52-2.580.30381560.27192960X-RAY DIFFRACTION99.3
2.58-2.640.30941530.26072923X-RAY DIFFRACTION99.42
2.64-2.710.35681560.26462968X-RAY DIFFRACTION99.21
2.71-2.790.29371560.27532960X-RAY DIFFRACTION99.17
2.79-2.880.33241550.27912946X-RAY DIFFRACTION98.76
2.88-2.990.30861550.27142938X-RAY DIFFRACTION98.75
2.99-3.110.27381550.25222956X-RAY DIFFRACTION98.86
3.11-3.250.31821560.24422946X-RAY DIFFRACTION98.1
3.25-3.420.27261530.23512918X-RAY DIFFRACTION97
3.42-3.630.24271570.21572984X-RAY DIFFRACTION98.96
3.63-3.910.22151570.18972985X-RAY DIFFRACTION98.84
3.91-4.310.19191590.17223010X-RAY DIFFRACTION99.03
4.31-4.930.18481570.16082983X-RAY DIFFRACTION98.12
4.93-6.210.2171580.18323014X-RAY DIFFRACTION97.15
6.21-49.290.19931620.17743061X-RAY DIFFRACTION94.29
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)
13.709433575950.286259722482-0.5311217971911.860271517410.2222572792813.20982349332-0.0484284139442-1.10036563511-0.5659359290570.220569606513-0.00855737984642-0.8046283809060.6561441882321.351712721780.04820210517330.5473505397160.307386858045-0.09240472509771.273794806320.02882048870270.81326226059944.484016724910.188537051846.1625848197
22.89540223454-0.384663145331-0.2050620432341.64651504222-0.2205042659241.665503302820.0350411470894-0.1116696080790.255332965098-0.3168530604760.180108621393-0.828036218079-0.2342179645050.765961928442-0.05052971312380.545296519312-0.1478548664730.1230578864520.782428864417-0.1534919832760.75936775294446.546125246332.307506499723.1637001084
30.4912275357650.00397833642916-0.4364203958262.509061201520.06820123224662.4547201781-0.0249277142336-0.2190175486750.01778127139930.3393827968510.0559966988932-0.04070209214920.1060884671770.276380267876-0.0272915604570.3336095064290.0426471892206-0.03715924703540.450226765895-0.04115527784470.35596040225716.013881256917.913302753755.0258438046
42.511262035092.208455995980.7560687592362.2393931866-0.9091826638372.90965352860.155375233991-0.2261670989260.4058840792470.3129356792530.103536658746-0.00967462619563-0.229547702537-0.101985770242-0.07555035056790.479459211092-0.0174569692013-0.005746209485380.36315899364-0.01307568840750.3914058499737.2366793625-4.4806196900834.1068753351
53.54985162459-0.4376258940491.353827586422.628941687590.7085548835272.543818736270.0696067354682-0.0470194779567-0.0711486411180.0884685804089-0.01645696557040.03292753723270.180446818010.00331651868131-0.07272643121910.442628155448-0.02158434622880.01624820866070.413732940918-0.01873653017740.41595840970357.4663543972-15.00968430476.8286828264
62.063448941470.0596404879445-0.8956895819971.41585772903-0.03015098350562.239448251630.13253103663-0.1673846495960.0837606002906-0.0319992718505-0.0519921814714-0.0558422120469-0.06053359395330.172867771543-0.07098843445590.488066830769-0.007433593490230.01256051483110.385663459396-0.06640675480430.41004700722926.1314773812-3.595224780399.4130812644
7-0.236515906931-0.414029654033-0.4811228819372.803694953010.7996766760750.3500212061830.0860519523436-0.2550804840860.2195038802140.328493134694-0.0494697542237-0.0875652556016-0.154384761165-0.0481441830778-0.01511340445050.416170010658-0.038354933989-0.02957384823850.27779944435-0.008651075236430.3760690061445.21336271688-33.794163340715.5223395041
80.5964381364180.2000077151320.04112670803971.34670339551.937434485961.62890785711-0.012330355079-0.03410403222880.0242587232604-0.243265480455-0.0160566056265-0.0822872610152-0.0372494598307-0.110174203370.02529301082790.4917937016750.00896246775973-0.01056156414310.4700107789040.02313851790460.4268442007714.41070225396-16.977106953824.8598685629
9-0.0625226773290.22913922642-0.2703820210041.9443529170.3445205895021.603033809140.00407690258361-0.02213594697370.05467141522220.01775489034570.01582353600570.288464912703-0.0629852261075-0.0547315952424-0.0318029520360.2789215375520.00211626571174-0.007218476618830.400652570938-0.02595532808270.3991552464195.3393769256820.772024480146.0028930899
101.28535855764-0.0740420671873-0.4451607112570.758704541639-0.1909275255791.155122995930.06514339442460.000387671117930.114599017949-0.3192149098250.0834806798076-0.00933681665776-0.2482014563560.0640666907856-0.09861643556040.451053926318-0.05745295480190.002963524548430.378664999642-0.04625496832150.42371485963220.390185732331.052167477224.7355850785
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 - 265
33chain 'A' and ((resseq 309:478))309 - 478266 - 435
44chain 'A' and ((resseq 479:524))479 - 524436 - 481
55chain 'A' and ((resseq 544:661))544 - 661482 - 599
66chain 'A' and ((resseq 662:767))662 - 767600 - 705
77chain 'A' and ((resseq 768:828))768 - 828706 - 744
88chain 'A' and ((resseq 829:912))829 - 912745 - 828
99chain 'A' and ((resseq 925:1061))925 - 1061841 - 965
1010chain 'A' and ((resseq 1062:1193))1062 - 1193966 - 1097

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