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- PDB-4k44: Auto-inhibition and phosphorylation-induced activation of PLC-gam... -

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Basic information

Entry
Database: PDB / ID: 4k44
TitleAuto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / SH2 domain / PLC-gamma1
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 / inositol trisphosphate biosynthetic process / VEGFR2 mediated cell proliferation / calcium-dependent phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / RET signaling / inositol trisphosphate metabolic process / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / response to gravity / phosphatidylinositol metabolic process / phospholipase C activity / COP9 signalosome / phosphatidylinositol phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / clathrin-coated vesicle / positive regulation of vascular endothelial cell proliferation / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / positive regulation of blood vessel endothelial cell migration / glutamate receptor binding / release of sequestered calcium ion into cytosol / ruffle / 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 / calcium-mediated signaling / insulin receptor binding / modulation of chemical synaptic transmission / epidermal growth factor receptor signaling pathway / response to hydrogen peroxide / Schaffer collateral - CA1 synapse / receptor tyrosine kinase binding / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / glutamatergic synapse / calcium ion binding / protein kinase binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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 ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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 / SH2 domain / SHC Adaptor Protein / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
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: 1.7 Å
AuthorsHajicek, N. / Sondek, J.
CitationJournal: Biochemistry / Year: 2013
Title: Autoinhibition and Phosphorylation-Induced Activation of Phospholipase C-gamma Isozymes.
Authors: Hajicek, N. / Charpentier, T.H. / Rush, J.R. / Harden, T.K. / Sondek, J.
History
DepositionApr 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)24,8762
Polymers24,8762
Non-polymers00
Water1,856103
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)12,4381
Polymers12,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)12,4381
Polymers12,4381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.106, 53.337, 150.281
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 12438.193 Da / Num. of mol.: 2 / Fragment: C-terminal SH2 (cSH2) domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Production host: Escherichia coli (E. coli)
References: UniProt: P10686, phosphoinositide phospholipase C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM MES, 200 mM ammonium acetate, 25% (w/v) PEG 4.000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→35.7 Å / Num. all: 175524 / Num. obs: 21853 / % possible obs: 99.3 % / Observed criterion σ(F): 4.7 / Observed criterion σ(I): 4.7 / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 0.463 / % possible all: 91.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QGI

3qgi


Resolution: 1.7→35.7 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2225 1120 5.13 %random
Rwork0.1821 ---
obs0.1843 21816 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 0 103 1817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071758
X-RAY DIFFRACTIONf_angle_d1.092360
X-RAY DIFFRACTIONf_dihedral_angle_d15.369686
X-RAY DIFFRACTIONf_chiral_restr0.081243
X-RAY DIFFRACTIONf_plane_restr0.005306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6941-1.77120.27341130.20872456X-RAY DIFFRACTION95
1.7712-1.86450.24131490.19812544X-RAY DIFFRACTION100
1.8645-1.98140.22081350.1992603X-RAY DIFFRACTION100
1.9814-2.13430.23951520.17942556X-RAY DIFFRACTION100
2.1343-2.34910.2391260.18762593X-RAY DIFFRACTION100
2.3491-2.68890.26191430.19122603X-RAY DIFFRACTION100
2.6889-3.38730.23271460.19322614X-RAY DIFFRACTION100
3.3873-35.73060.18931560.1622727X-RAY DIFFRACTION99
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)
13.9174-1.32410.1128.10111.51644.72980.0143-0.13020.140.3425-0.06680.0614-0.156-0.1930.05380.12960.0451-0.01140.14970.0020.147-20.112311.542525.3165
22.82693.37060.18486.2955-0.96554.7715-0.08310.0772-0.0024-0.45590.06580.0519-0.26440.12260.05290.16680.06740.00570.153-0.01850.1111-10.73074.43614.9878
30.50541.0580.59362.23681.46743.00330.07441.1481-0.192-0.183-0.0609-0.4186-0.57030.34890.10790.1717-0.06160.02550.4419-0.01010.2056-2.670313.014818.7121
43.5373-0.2047-2.03343.3687-0.41948.4907-0.31620.0474-0.3220.00630.15230.4260.8898-0.39180.16290.17860.02890.02120.1560.01130.152-17.99982.905826.9695
53.4779-0.799-1.11852.9744-0.72332.9819-0.03290.0059-0.1790.05970.0379-0.46150.14370.34870.00410.11450.04370.00170.2334-0.02660.1895-7.82915.427925.3528
67.4175-1.3663-5.59342.40432.28087.876-0.1273-0.57640.1240.2080.2062-0.26520.65460.53760.10570.20820.07-0.00430.18780.02680.1956-13.23293.218333.1472
73.18610.68162.63237.9977-2.3643.2659-0.0487-0.679-0.29010.5577-0.0322-0.02530.49090.76540.1860.29260.0870.0050.39970.03710.1237-12.84987.678340.981
87.14180.594-0.12554.4703-0.22475.45390.24970.04350.17660.1639-0.2935-0.1479-0.51630.27950.05980.1996-0.0035-0.03650.1416-0.00390.1052-7.001612.365133.7803
92.7696-2.82810.80413.0414-1.42712.68830.02980.47860.35890.0404-0.1651-0.1216-0.19730.6078-0.15750.1534-0.0043-0.03070.26760.00810.1792-6.564914.190623.8905
101.84571.7981.68952.14071.53653.80940.07120.4569-0.70120.00820.00460.17270.17760.132-0.52551.01570.1712-0.24850.98130.04970.6626-22.1388.00047.9275
112.9876-0.25371.35913.5837-0.52654.5696-0.0661-0.04920.07260.04890.12490.0076-0.1061-0.2323-0.02560.14460.05740.00990.0951-0.00630.1295-34.237723.144212.5493
125.30751.405-0.03921.0926-0.11022.326-0.0142-0.5629-0.3350.33260.05850.19750.0527-0.27290.02040.17740.09070.00480.17720.01120.159-28.096212.853622.7124
131.23271.81992.7082.96284.22726.1391-0.1284-0.8051-0.661.2015-0.13030.15831.3541-0.60270.27220.4047-0.02190.0560.26370.05520.2887-37.26935.989718.9756
144.26540.7073-2.80754.7553-2.20156.12270.1645-0.2960.4807-0.016-0.2484-0.268-0.06440.83930.06440.14420.03040.00570.19820.03560.1926-25.328720.254310.7619
153.1254-1.45380.24435.6802-3.08765.1425-0.0285-0.0175-0.4902-0.272-0.0917-0.17060.56150.07160.10620.19570.05350.00010.16390.02870.2099-27.028112.049810.2461
163.77542.18711.31643.31530.94340.475-0.16660.4494-0.2529-0.62220.2276-0.3530.59960.3781-0.05350.34670.04970.06430.1762-0.00220.1397-29.515317.5712-2.9728
173.11971.0047-0.53597.5364-0.17872.1463-0.12570.0245-0.3498-0.1570.23280.16570.8035-0.2553-0.160.3105-0.04410.00490.13110.01360.1605-36.34249.21634.5414
186.6944-0.5988-2.85855.1379-4.24525.2049-0.03720.1131-0.4396-0.31570.1737-0.24220.7439-0.8348-0.07190.1764-0.04220.00940.15990.00120.2107-39.596610.211914.2225
194.10544.20355.66254.39795.64428.06030.6532-0.4473-0.21350.69570.2439-1.25870.10910.3739-0.83610.52240.0718-0.04030.5535-0.1060.4757-32.138623.465628.1292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 661 through 674 )
2X-RAY DIFFRACTION2chain 'A' and (resid 675 through 684 )
3X-RAY DIFFRACTION3chain 'A' and (resid 685 through 690 )
4X-RAY DIFFRACTION4chain 'A' and (resid 691 through 700 )
5X-RAY DIFFRACTION5chain 'A' and (resid 701 through 710 )
6X-RAY DIFFRACTION6chain 'A' and (resid 711 through 726 )
7X-RAY DIFFRACTION7chain 'A' and (resid 727 through 733 )
8X-RAY DIFFRACTION8chain 'A' and (resid 734 through 748 )
9X-RAY DIFFRACTION9chain 'A' and (resid 749 through 758 )
10X-RAY DIFFRACTION10chain 'A' and (resid 759 through 764 )
11X-RAY DIFFRACTION11chain 'B' and (resid 661 through 674 )
12X-RAY DIFFRACTION12chain 'B' and (resid 675 through 684 )
13X-RAY DIFFRACTION13chain 'B' and (resid 685 through 690 )
14X-RAY DIFFRACTION14chain 'B' and (resid 691 through 700 )
15X-RAY DIFFRACTION15chain 'B' and (resid 701 through 720 )
16X-RAY DIFFRACTION16chain 'B' and (resid 721 through 733 )
17X-RAY DIFFRACTION17chain 'B' and (resid 734 through 751 )
18X-RAY DIFFRACTION18chain 'B' and (resid 752 through 756 )
19X-RAY DIFFRACTION19chain 'B' and (resid 757 through 765 )

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