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- PDB-1ywo: Phospholipase Cgamma1 SH3 in complex with a SLP-76 motif -

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Basic information

Entry
Database: PDB / ID: 1ywo
TitlePhospholipase Cgamma1 SH3 in complex with a SLP-76 motif
Components
  • 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 1
  • Lymphocyte cytosolic protein 2
KeywordsHYDROLASE / SIGNALING PROTEIN / SH3 / Phospholipase C-gamma1 / SLP-76 / SH2 domain-containing leukocyte phosphoprotein of 76 kD
Function / homology
Function and homology information


TCR signalosome / 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 ...TCR signalosome / 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 / mast cell activation / 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 / plasma membrane raft / Generation of second messenger molecules / glutamate receptor binding / positive regulation of blood vessel endothelial cell migration / positive regulation of protein kinase activity / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / ruffle / GPVI-mediated activation cascade / response to organonitrogen compound / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / positive regulation of release of sequestered calcium ion into cytosol / cell projection / calcium-mediated signaling / FCERI mediated MAPK activation / phosphoprotein binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / response to hydrogen peroxide / insulin receptor binding / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / ruffle membrane / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of angiogenesis / calcium ion transport / cell-cell junction / cell migration / DAP12 signaling / lamellipodium / T cell receptor signaling pathway / in utero embryonic development / intracellular signal transduction / immune response / 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. / SAM domain (Sterile alpha motif) / SH3 Domains / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / 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 / SH3 type barrels. / 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 / Lymphocyte cytosolic protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsDeng, L. / Velikovsky, C.A. / Swaminathan, C.P. / Cho, S. / Mariuzza, R.A.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Basis for Recognition of the T Cell Adaptor Protein SLP-76 by the SH3 Domain of Phospholipase Cgamma1
Authors: Deng, L. / Velikovsky, C.A. / Swaminathan, C.P. / Cho, S. / Mariuzza, R.A.
History
DepositionFeb 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 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 1.4Feb 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
P: Lymphocyte cytosolic protein 2


Theoretical massNumber of molelcules
Total (without water)8,5622
Polymers8,5622
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.723, 46.723, 58.112
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 7414.259 Da / Num. of mol.: 1 / Mutation: C5S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Plcg1 / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P10686, phosphoinositide phospholipase C
#2: Protein/peptide Lymphocyte cytosolic protein 2 / / SH2 domain-containing leucocyte protein of 76 kDa / SLP-76 tyrosine phosphoprotein / SLP76


Mass: 1147.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13094
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.9 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: malonate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.009 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. obs: 6149 / Rmerge(I) obs: 0.097 / Net I/σ(I): 21.7
Reflection shellResolution: 1.81→1.87 Å / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8 / % possible all: 85.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→36.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.412 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22129 279 4.6 %RANDOM
Rwork0.17063 ---
obs0.17285 5831 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.064 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.81→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 0 67 603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.946761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.84424.51631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.641597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.613154
X-RAY DIFFRACTIONr_chiral_restr0.0950.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2226
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2375
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6672331
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5443527
X-RAY DIFFRACTIONr_scbond_it1.7392275
X-RAY DIFFRACTIONr_scangle_it2.6453234
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.805→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 15 -
Rwork0.269 327 -
obs--77.2 %
Refinement TLS params.Method: refined / Origin x: 20.4361 Å / Origin y: 11.5163 Å / Origin z: 17.5977 Å
111213212223313233
T-0.0418 Å20.0036 Å2-0.0041 Å2--0.0038 Å2-0.0233 Å2---0.023 Å2
L2.5795 °21.7207 °2-0.2661 °2-2.211 °2-0.7526 °2--4.0509 °2
S-0.019 Å °-0.0011 Å °0.1814 Å °-0.0076 Å °0.0482 Å °0.1718 Å °-0.0291 Å °-0.1294 Å °-0.0292 Å °

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