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- PDB-4k45: Auto-inhibition and phosphorylation-induced activation of PLC-gam... -

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Basic information

Entry
Database: PDB / ID: 4k45
TitleAuto-inhibition and phosphorylation-induced activation of PLC-gamma isozymes
Components
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
  • 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, short peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SH2 domain / PLC-gamma1 / HYDROLASE-HYDROLASE INHIBITOR complex
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 / inositol trisphosphate biosynthetic process ...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 / inositol trisphosphate biosynthetic process / ISG15 antiviral mechanism / Downstream signal transduction / Signaling by ALK / Generation of second messenger molecules / Role of phospholipids in phagocytosis / lysophospholipase C activity / DAP12 signaling / FCERI mediated Ca+2 mobilization / VEGFR2 mediated cell proliferation / RET signaling / Synthesis of IP3 and IP4 in the cytosol / inositol trisphosphate metabolic process / phosphatidylinositol phospholipase C activity / regulation of store-operated calcium channel activity / response to curcumin / phosphoinositide phospholipase C / FCERI mediated MAPK activation / phosphatidylinositol metabolic process / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / neurotrophin TRKA receptor binding / C-type glycerophospholipase activity / COP9 signalosome / positive regulation of vascular endothelial cell proliferation / clathrin-coated vesicle / positive regulation of wound healing / positive regulation of cell size / response to gravity / 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 / release of sequestered calcium ion into cytosol / ruffle / cell projection / in utero embryonic development / guanyl-nucleotide exchange factor activity / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / insulin receptor binding / calcium-mediated signaling / response to hydrogen peroxide / phosphoprotein binding / receptor tyrosine kinase binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / epidermal growth factor receptor signaling pathway / T cell receptor signaling pathway / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / lamellipodium / positive regulation of cell migration / 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 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / : / : / PLCG EF-hand motif 1 / PLCG EF-hand motif 2 / Phosphoinositide phospholipase C family / Phospholipase C, phosphatidylinositol-specific, Y 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 / : / : / PLCG EF-hand motif 1 / 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 / SH2 domain / SHC Adaptor Protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / PH domain / PH domain profile. / C2 domain superfamily / 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 / Src homology 3 (SH3) domain profile. / SH3 domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / 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: 1.5 Å
AuthorsSondek, J. / Hajicek, N.
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 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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, short peptide


Theoretical massNumber of molelcules
Total (without water)14,5542
Polymers14,5542
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-5 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.013, 54.506, 59.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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


Mass: 2116.119 Da / Num. of mol.: 1 / Fragment: residues 770 to 787 of PLC-gamma1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
References: UniProt: P10686, phosphoinositide phospholipase C
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
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: 1.63 Å3/Da / Density % sol: 24.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 100 mM MES, 200 mM ammonium acetate, 35% (w/v) PEG 4,000, microseeding, pH 6.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 116025 / Num. obs: 15900 / % possible obs: 99.8 % / Observed criterion σ(F): 3.8 / Observed criterion σ(I): 3.8
Reflection shellResolution: 1.5→1.53 Å / % possible all: 97.4

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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 / Resolution: 1.5→40.303 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.198 790 4.98 %random
Rwork0.1729 ---
obs0.1629 15850 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→40.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms900 0 0 80 980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015940
X-RAY DIFFRACTIONf_angle_d1.631262
X-RAY DIFFRACTIONf_dihedral_angle_d13.364367
X-RAY DIFFRACTIONf_chiral_restr0.121125
X-RAY DIFFRACTIONf_plane_restr0.007164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4979-1.59180.22691220.18272444X-RAY DIFFRACTION99
1.5918-1.71470.2071170.17672491X-RAY DIFFRACTION100
1.7147-1.88730.18611360.16762456X-RAY DIFFRACTION100
1.8873-2.16030.22831470.15472486X-RAY DIFFRACTION100
2.1603-2.72170.20081510.16352507X-RAY DIFFRACTION100
2.7217-40.31780.1771170.15382676X-RAY DIFFRACTION100
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)
10.0282-0.0132-0.11271.04350.41290.5831-0.01930.0070.07050.10910.01530.17260.0764-0.1819-0.36360.05490.00170.01450.1126-0.00230.1009-17.02956.0085-1.3382
20.96030.66980.65810.78740.96251.2430.0918-0.1875-0.27050.3017-0.0745-0.12990.41490.03190.05020.16550.0111-0.01410.08540.00360.1098-9.7683-6.7001-1.8319
30.56430.2166-0.51392.7277-1.66291.28040.05620.0236-0.0030.17390.13930.08090.07970.04860.28950.0814-0.0111-0.00840.0553-0.02020.0568-17.6255-7.1928-10.9759
40.2457-0.0119-0.06490.1069-0.23770.56250.01610.0349-0.08350.06040.0193-0.1290.03230.01230.06080.0426-0.0061-0.01410.0467-0.01680.0638-7.6084.1946-5.3508
50.2098-0.39080.00530.79370.07350.1073-0.0420.1627-0.0139-0.12040.1569-0.288-0.05950.06680.01320.0955-0.0038-00.0944-0.03170.0989-5.02466.1204-9.5747
60.0142-0.2253-0.01943.63540.31450.02720.0440.13330.1313-0.48160.0559-0.5084-0.21950.2307-0.05610.1098-0.0029-0.00220.1087-0.0050.1285-7.729217.72-9.4061
70.9422-0.2564-0.68980.07080.20560.8666-0.0662-0.10490.1884-0.12820.0484-0.125-0.02110.30110.00690.11420.00440.01130.07180.00370.0855-10.583616.4677-13.9873
80.7241-0.17721.13050.3979-0.49092.5582-0.071-0.1033-0.0594-0.05170.07040.2478-0.0215-0.30250.00610.08680.0042-0.00240.05490.00410.0726-16.97810.6262-12.737
90.06570.2327-0.03960.839-0.13760.0247-0.05360.0448-0.0175-0.2989-0.0382-0.01270.11430.057-0.01720.13030.01820.00370.1246-0.01970.1044-15.93910.9151-14.9647
100.7519-0.9259-0.56371.14110.69530.424-0.19430.065-0.2550.3583-0.09170.27380.5033-0.0193-0.04650.43920.05230.09920.4740.16980.3445-23.006-6.04411.7173
110.4407-0.34590.32771.6858-0.81380.47810.00490.39910.0334-0.3772-0.164-0.24180.1550.3628-0.030.16880.0091-0.00170.2506-0.03090.2123-1.5622.1994-12.9792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 662 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 710 )
5X-RAY DIFFRACTION5chain 'A' and (resid 711 through 720 )
6X-RAY DIFFRACTION6chain 'A' and (resid 721 through 726 )
7X-RAY DIFFRACTION7chain 'A' and (resid 727 through 733 )
8X-RAY DIFFRACTION8chain 'A' and (resid 734 through 743 )
9X-RAY DIFFRACTION9chain 'A' and (resid 744 through 757 )
10X-RAY DIFFRACTION10chain 'A' and (resid 758 through 763 )
11X-RAY DIFFRACTION11chain 'B' and (resid 198 through 205 )

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