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- PDB-4fbn: Insights into structural integration of the PLCgamma regulatory r... -

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Basic information

Entry
Database: PDB / ID: 4fbn
TitleInsights into structural integration of the PLCgamma regulatory region and mechanism of autoinhibition and activation based on key roles of SH2 domains
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 / phosphoinositide phospholipase C / Role of second messengers in netrin-1 signaling / DAG and IP3 signaling / phospholipid catabolic process / phosphatidylinositol metabolic process / Phospholipase C-mediated cascade; FGFR3 ...Activated NTRK3 signals through PLCG1 / Activated NTRK2 signals through PLCG1 / calcium-dependent phospholipase C activity / PLC-gamma1 signalling / phosphoinositide phospholipase C / Role of second messengers in netrin-1 signaling / DAG and IP3 signaling / phospholipid catabolic process / phosphatidylinositol metabolic process / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR4 / phosphatidylinositol phospholipase C activity / Erythropoietin activates Phospholipase C gamma (PLCG) / COP9 signalosome / Phospholipase C-mediated cascade: FGFR1 / phospholipase C activity / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / phosphatidylinositol-mediated signaling / EGFR interacts with phospholipase C-gamma / positive regulation of vascular endothelial cell proliferation / PLCG1 events in ERBB2 signaling / Signaling by ALK / positive regulation of epithelial cell migration / Synthesis of IP3 and IP4 in the cytosol / Fc-epsilon receptor signaling pathway / PECAM1 interactions / Generation of second messenger molecules / Signaling by ALK fusions and activated point mutants / RET signaling / glutamate receptor binding / positive regulation of blood vessel endothelial cell migration / Role of phospholipids in phagocytosis / Signaling by FGFR4 in disease / release of sequestered calcium ion into cytosol / negative regulation of inflammatory response to antigenic stimulus / Signaling by FGFR3 in disease / cellular response to epidermal growth factor stimulus / ruffle / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / Downstream signal transduction / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / FCGR3A-mediated IL10 synthesis / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / modulation of chemical synaptic transmission / Constitutive Signaling by EGFRvIII / Schaffer collateral - CA1 synapse / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / receptor tyrosine kinase binding / ISG15 antiviral mechanism / ruffle membrane / positive regulation of angiogenesis / cell migration / cell-cell junction / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / 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 / SH2 domain / SHC Adaptor Protein / C2 domain / Protein kinase C conserved region 2 (CalB) / 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 / 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 / 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: 2.4 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 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)28,5781
Polymers28,5781
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.752, 59.610, 76.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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: 28578.170 Da / Num. of mol.: 1
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 / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 22% PEG 5K MME, 0.1M Na Malonate 20mM CaCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9163 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9163 Å / Relative weight: 1
ReflectionResolution: 2.4→44.06 Å / % possible obs: 96.2 % / Observed criterion σ(F): 1.25 / Observed criterion σ(I): 2.5 / Biso Wilson estimate: 69.11 Å2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.695 / % possible all: 96.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→44.06 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.8732 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2954 451 4.75 %RANDOM
Rwork0.2187 ---
obs0.2224 9496 93.61 %-
Displacement parametersBiso mean: 79.02 Å2
Baniso -1Baniso -2Baniso -3
1--15.5756 Å20 Å20 Å2
2--10.9466 Å20 Å2
3---4.6289 Å2
Refine analyzeLuzzati coordinate error obs: 0.458 Å
Refinement stepCycle: LAST / Resolution: 2.4→44.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 0 32 1834
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013485HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116230HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d726SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes40HARMONIC2
X-RAY DIFFRACTIONt_gen_planes554HARMONIC5
X-RAY DIFFRACTIONt_it3485HARMONIC20
X-RAY DIFFRACTIONt_nbd
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: 2.4→2.68 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3232 124 4.81 %
Rwork0.2231 2456 -
all0.2275 2580 -
obs--93.61 %
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)
13.92923.4561.535212.72632.08664.6526-0.21390.1401-0.11550.08340.1254-0.59480.00420.09720.0885-0.15840.06130.0057-0.22990.0127-0.169610.7709-8.45944.0756
24.27574.08225.53855.96283.892410.97560.1111-0.35850.25540.5097-0.0473-0.80010.05510.4948-0.06380.02120.0742-0.304-0.26030.05170.282621.4173-7.233214.0024
30.5742-0.0471-2.18555.6883-3.66958.3359-0.03650.1652-0.0125-0.91160.0207-0.4866-0.19520.47610.0158-0.0193-0.01830.2109-0.3273-0.0711-0.171414.554-14.5172-21.4312
43.6071-0.1227-0.91277.74031.76354.54430.2208-0.1874-0.1214-0.49530.0194-0.43970.40940.258-0.24020.0459-0.01510.209-0.315-0.05-0.18215.4523-21.2148-23.3938
50.64812.93481.39882.03170.57460.0205-0.0334-0.0617-0.0012-0.0559-0.00980.14370.14260.03650.04320.0965-0.14120.0604-0.20560.16160.079910.8326-31.5397-23.7108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|547 - A|612 }A547 - 612
2X-RAY DIFFRACTION2{ A|613 - A|652 }A613 - 652
3X-RAY DIFFRACTION3{ A|653 - A|696 }A653 - 696
4X-RAY DIFFRACTION4{ A|697 - A|771 }A697 - 771
5X-RAY DIFFRACTION5{ A|783 - A|789 }A783 - 789

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