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- PDB-4ey0: Structure of tandem SH2 domains from PLCgamma1 -

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Basic information

Entry
Database: PDB / ID: 4ey0
TitleStructure of tandem SH2 domains from PLCgamma1
Components1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
KeywordsHYDROLASE / SH2 Domain / PLCgamma specific array / Interaction Domain / fibroblast growth factor receptor 1
Function / homology
Function and homology information


Activated NTRK3 signals through PLCG1 / Activated NTRK2 signals through PLCG1 / calcium-dependent phospholipase C activity / PLC-gamma1 signalling / Role of second messengers in netrin-1 signaling / DAG and IP3 signaling / phosphoinositide phospholipase C / Phospholipase C-mediated cascade; FGFR3 / phosphatidylinositol metabolic process / Phospholipase C-mediated cascade; FGFR2 ...Activated NTRK3 signals through PLCG1 / Activated NTRK2 signals through PLCG1 / calcium-dependent phospholipase C activity / PLC-gamma1 signalling / Role of second messengers in netrin-1 signaling / DAG and IP3 signaling / phosphoinositide phospholipase C / Phospholipase C-mediated cascade; FGFR3 / phosphatidylinositol metabolic process / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR4 / COP9 signalosome / Erythropoietin activates Phospholipase C gamma (PLCG) / phospholipase C activity / neurotrophin TRKA receptor binding / Phospholipase C-mediated cascade: FGFR1 / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / phospholipid catabolic process / positive regulation of vascular endothelial cell proliferation / EGFR interacts with phospholipase C-gamma / PLCG1 events in ERBB2 signaling / Signaling by ALK / phosphatidylinositol-mediated signaling / Synthesis of IP3 and IP4 in the cytosol / Fc-epsilon receptor signaling pathway / PECAM1 interactions / RET signaling / Generation of second messenger molecules / positive regulation of epithelial cell migration / positive regulation of endothelial cell apoptotic process / positive regulation of blood vessel endothelial cell migration / Role of phospholipids in phagocytosis / glutamate receptor binding / Signaling by FGFR4 in disease / Signaling by FGFR3 in disease / ruffle / Signaling by FGFR2 in disease / release of sequestered calcium ion into cytosol / Signaling by FGFR1 in disease / FCERI mediated Ca+2 mobilization / Downstream signal transduction / cellular response to epidermal growth factor stimulus / FCGR3A-mediated IL10 synthesis / positive regulation of release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / VEGFR2 mediated cell proliferation / cell projection / FCERI mediated MAPK activation / negative regulation of inflammatory response to antigenic stimulus / modulation of chemical synaptic transmission / Signaling by ERBB2 TMD/JMD mutants / calcium-mediated signaling / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Schaffer collateral - CA1 synapse / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / ISG15 antiviral mechanism / epidermal growth factor receptor signaling pathway / ruffle membrane / positive regulation of angiogenesis / Signaling by ALK fusions and activated point mutants / DAP12 signaling / cell-cell junction / cell migration / lamellipodium / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / T cell receptor signaling pathway / in utero embryonic development / 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 / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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. ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, SH3 domain / PLCG EF-hand motif 1 / Phosphatidylinositol-4, 5-bisphosphate phosphodiesterase gamma / PLC-gamma, C-terminal SH2 domain / PLC-gamma, N-terminal SH2 domain / 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 / 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 / SH2 domain superfamily / Src homology 3 domains / EF-Hand 1, calcium-binding site / SH3-like domain superfamily / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCole, A.R. / Mas-Droux, C.P. / Bunney, T.D. / Katan, M.
CitationJournal: Structure / Year: 2012
Title: Structural and Functional Integration of the PLCgamma Interaction Domains Critical for Regulatory Mechanisms and Signaling Deregulation.
Authors: Bunney, T.D. / Esposito, D. / Mas-Droux, C. / Lamber, E. / Baxendale, R.W. / Martins, M. / Cole, A. / Svergun, D. / Driscoll, P.C. / Katan, M.
History
DepositionMay 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 20, 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
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)114,5054
Polymers114,5054
Non-polymers00
Water2,936163
1
A: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)28,6261
Polymers28,6261
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)28,6261
Polymers28,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)28,6261
Polymers28,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1


Theoretical massNumber of molelcules
Total (without water)28,6261
Polymers28,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.900, 59.200, 79.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28626.146 Da / Num. of mol.: 4 / Mutation: Y771F, Y775F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLC1, PLCG1 / Production host: Escherichia coli (E. coli)
References: UniProt: P19174, phosphoinositide phospholipase C
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 8000, 0.1M HEPES.Na, 0.2M Calcium Acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.795→47.42 Å / Num. all: 22779 / Num. obs: 22779 / % possible obs: 92.1 % / Observed criterion σ(F): 0.55 / Observed criterion σ(I): 1.1 / Redundancy: 2 % / Biso Wilson estimate: 73.93 Å2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-2.9520.7621.1192.1
8.84-47.4720.02117.199.4

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→47.42 Å / Cor.coef. Fo:Fc: 0.9171 / Cor.coef. Fo:Fc free: 0.8913 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 1152 5.07 %RANDOM
Rwork0.197 ---
obs0.1992 22717 92.33 %-
all-2717 --
Displacement parametersBiso mean: 53.41 Å2
Baniso -1Baniso -2Baniso -3
1--2.2244 Å20.5322 Å20.499 Å2
2--6.0296 Å2-1.1138 Å2
3----3.8052 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7510 0 0 163 7673
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114625HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1626177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3090SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes198HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2285HARMONIC5
X-RAY DIFFRACTIONt_it14625HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.8→2.94 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3259 146 4.52 %
Rwork0.2204 3085 -
all0.2252 3231 -
obs--92.33 %

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