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- PDB-1y0m: Crystal structure of of the SH3 domain of phospholipase C Gamma-1 -

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Basic information

Entry
Database: PDB / ID: 1y0m
TitleCrystal structure of of the SH3 domain of phospholipase C Gamma-1
Components1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1
KeywordsHYDROLASE / SH3 domain
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 / FCERI mediated Ca+2 mobilization / 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 / FCERI mediated Ca+2 mobilization / ISG15 antiviral mechanism / Generation of second messenger molecules / Phospholipase C-mediated cascade; FGFR2 / Downstream signal transduction / Signaling by ALK / Role of phospholipids in phagocytosis / inositol trisphosphate biosynthetic process / DAP12 signaling / 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 / phosphatidylinositol phospholipase C activity / COP9 signalosome / phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / phosphatidylinositol-mediated signaling / positive regulation of vascular endothelial cell proliferation / clathrin-coated vesicle / positive regulation of epithelial cell migration / glutamate receptor binding / positive regulation of blood vessel endothelial cell migration / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / ruffle / response to organonitrogen compound / guanyl-nucleotide exchange factor activity / positive regulation of release of sequestered calcium ion into cytosol / cell projection / calcium-mediated signaling / phosphoprotein binding / modulation of chemical synaptic transmission / response to hydrogen peroxide / Schaffer collateral - CA1 synapse / insulin receptor binding / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / ruffle membrane / positive regulation of angiogenesis / calcium ion transport / cell migration / cell-cell junction / 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 X-box domain profile. ...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 X-box domain profile. / Phosphatidylinositol-specific phospholipase C, X domain / Phosphatidylinositol-specific phospholipase C, X domain / Phospholipase C, catalytic domain (part); domain X / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / SH3 Domains / 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 / SH3 type barrels. / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / SH2 domain superfamily / 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 / Roll / Mainly 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: 1.2 Å
AuthorsMariuzza, R. / Sangwoo, C.
CitationJournal: To be Published
Title: Crystal structure of of the SH3 domain of phospholipase C Gamma-1
Authors: Mariuzza, R. / Sangwoo, C.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)7,1731
Polymers7,1731
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.748, 30.978, 29.753
Angle α, β, γ (deg.)90.00, 92.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1 / Phosphoinositide phospholipase C / PLC-gamma-1 / Phospholipase C-gamma-1 / PLC-II / PLC-148


Mass: 7173.015 Da / Num. of mol.: 1 / Fragment: SH3 domain: sequence database residues 791-851 / Mutation: C794S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli)
References: UniProt: P10686, phosphoinositide phospholipase C
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tacsimate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 16059 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.077 / Χ2: 2.144
Reflection shellResolution: 1.2→1.24 Å / Rmerge(I) obs: 0.181 / Num. unique all: 1302 / Χ2: 2.176 / % possible all: 79

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Phasing

Phasing MRRfactor: 0.395 / Cor.coef. Fo:Fc: 0.592
Highest resolutionLowest resolution
Rotation3 Å29.73 Å
Translation3 Å29.73 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.501data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→29.75 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.598 / SU ML: 0.028 / SU R Cruickshank DPI: 0.049 / Cross valid method: THROUGHOUT / ESU R Free: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.177 808 5.1 %RANDOM
Rwork0.151 ---
all0.153 ---
obs-15999 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.503 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20.36 Å2
2---0.76 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.2→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms526 0 0 122 648
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.015320.022
X-RAY DIFFRACTIONr_bond_other_d0.0024490.02
X-RAY DIFFRACTIONr_angle_refined_deg1.2917141.916
X-RAY DIFFRACTIONr_angle_other_deg0.78710593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.459605
X-RAY DIFFRACTIONr_chiral_restr0.08690.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0075890.02
X-RAY DIFFRACTIONr_gen_planes_other0.0011140.02
X-RAY DIFFRACTIONr_nbd_refined0.222820.2
X-RAY DIFFRACTIONr_nbd_other0.2495170.2
X-RAY DIFFRACTIONr_nbtor_other0.0833040.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.238780.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.134170.2
X-RAY DIFFRACTIONr_symmetry_vdw_other0.232640.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.16390.2
X-RAY DIFFRACTIONr_mcbond_it0.9643021.5
X-RAY DIFFRACTIONr_mcangle_it1.5264842
X-RAY DIFFRACTIONr_scbond_it1.8152303
X-RAY DIFFRACTIONr_scangle_it2.7252304.5
X-RAY DIFFRACTIONRIGID-BOND RESTRAINTS (A**2)0.9695322
X-RAY DIFFRACTIONSPHERICITY; FREE ATOMS (A**2)1222.327
X-RAY DIFFRACTIONSPHERICITY; BONDED ATOMS (A**2)5191.94
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.338 48
Rwork0.191 888

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