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- PDB-2dx0: Crystal structure of the N-terminal SH2 domain of mouse phospholi... -

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Basic information

Entry
Database: PDB / ID: 2dx0
TitleCrystal structure of the N-terminal SH2 domain of mouse phospholipase C-gamma 2
ComponentsPhospholipase C, gamma 2
KeywordsHYDROLASE / PHOSPHORIC DIESTER HYDROLASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Dectin-2 family / inositol trisphosphate biosynthetic process / Toll Like Receptor 4 (TLR4) Cascade / phosphatidylcholine phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / GPVI-mediated activation cascade / regulation of calcineurin-NFAT signaling cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / follicular B cell differentiation ...Dectin-2 family / inositol trisphosphate biosynthetic process / Toll Like Receptor 4 (TLR4) Cascade / phosphatidylcholine phospholipase C activity / Synthesis of IP3 and IP4 in the cytosol / GPVI-mediated activation cascade / regulation of calcineurin-NFAT signaling cascade / FCERI mediated MAPK activation / Generation of second messenger molecules / follicular B cell differentiation / activation of store-operated calcium channel activity / Role of phospholipids in phagocytosis / positive regulation of dendritic cell cytokine production / phosphoinositide phospholipase C / antifungal innate immune response / FCERI mediated Ca+2 mobilization / cellular response to lectin / response to yeast / positive regulation of interleukin-23 production / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / CLEC7A (Dectin-1) signaling / phosphorylation-dependent protein binding / phosphatidylinositol metabolic process / positive regulation of cell cycle G1/S phase transition / positive regulation of macrophage cytokine production / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / cell activation / C-type glycerophospholipase activity / positive regulation of phagocytosis, engulfment / phosphatidylinositol biosynthetic process / macrophage activation involved in immune response / phospholipid catabolic process / cellular response to lipid / DAP12 signaling / regulation of canonical NF-kappaB signal transduction / negative regulation of programmed cell death / positive regulation of neuroinflammatory response / toll-like receptor signaling pathway / stimulatory C-type lectin receptor signaling pathway / response to ATP / positive regulation of reactive oxygen species biosynthetic process / intracellular vesicle / phosphatidylinositol-mediated signaling / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of epithelial cell migration / positive regulation of intracellular signal transduction / positive regulation of interleukin-10 production / response to axon injury / regulation of lipid metabolic process / B cell activation / positive regulation of receptor internalization / response to magnesium ion / positive regulation of interleukin-12 production / release of sequestered calcium ion into cytosol / positive regulation of calcium-mediated signaling / positive regulation of interleukin-2 production / lipopolysaccharide-mediated signaling pathway / phosphotyrosine residue binding / positive regulation of type I interferon production / B cell differentiation / cellular response to calcium ion / protein tyrosine kinase binding / B cell receptor signaling pathway / calcium-mediated signaling / positive regulation of interleukin-6 production / ruffle membrane / positive regulation of tumor necrosis factor production / T cell receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of gene expression / response to lipopolysaccharide / scaffold protein binding / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / membrane raft / positive regulation of gene expression / protein kinase binding / perinuclear region of cytoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, 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-2, 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 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 domain pair / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHanda, N. / Takagi, T. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the N-terminal SH2 domain of mouse phospholipase C-gamma 2
Authors: Takagi, T. / Handa, N. / Murayama, K. / Shirouzu, M. / Kurosaki, T. / Terada, T. / Yokoyama, S.
History
DepositionAug 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase C, gamma 2
B: Phospholipase C, gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6575
Polymers31,3692
Non-polymers2883
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-70 kcal/mol
Surface area11160 Å2
MethodPISA
2
A: Phospholipase C, gamma 2
hetero molecules

B: Phospholipase C, gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6575
Polymers31,3692
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area1410 Å2
ΔGint-52 kcal/mol
Surface area14720 Å2
MethodPISA
3
A: Phospholipase C, gamma 2
hetero molecules

A: Phospholipase C, gamma 2
hetero molecules

B: Phospholipase C, gamma 2
hetero molecules

B: Phospholipase C, gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,31410
Polymers62,7374
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
crystal symmetry operation6_555x+1/2,-y+1/2,-z+3/41
Buried area4590 Å2
ΔGint-118 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.905, 80.905, 133.734
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phospholipase C, gamma 2


Mass: 15684.371 Da / Num. of mol.: 2 / Fragment: N-terminal SH2 domain, residues 516-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PX060201-15 / Production host: Cell-free protein synthesis / References: UniProt: Q8CIH5
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: ammonium sulfate, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9791, 0.9794, 0.9700
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.971
ReflectionResolution: 2.5→50 Å / Num. obs: 15954 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 36.3 Å2 / Rsym value: 0.08 / Net I/σ(I): 22.8
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.289 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1436758.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 777 4.9 %RANDOM
Rwork0.222 ---
obs0.222 15901 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1326 Å2 / ksol: 0.378199 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.58 Å20 Å20 Å2
2--4.58 Å20 Å2
3----9.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 15 102 1872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.531.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 123 4.9 %
Rwork0.25 2404 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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