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- PDB-7nxe: Structure of the Phospholipase C gamma 1 tSH2 domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 7nxe
TitleStructure of the Phospholipase C gamma 1 tSH2 domain in complex with a phosphorylated KSHV pK15 peptide
Components
  • Isoform 2 of 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
  • Protein K15
KeywordsVIRAL PROTEIN / KSHV / complex / phosphorylation
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 / phosphoinositide phospholipase C / 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 / Role of second messengers in netrin-1 signaling / phosphoinositide phospholipase C / DAG and IP3 signaling / phospholipid catabolic process / phosphatidylinositol metabolic process / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR2 / phosphatidylinositol phospholipase C activity / Phospholipase C-mediated cascade; FGFR4 / Erythropoietin activates Phospholipase C gamma (PLCG) / COP9 signalosome / phospholipase C activity / Phospholipase C-mediated cascade: FGFR1 / neurotrophin TRKA receptor binding / positive regulation of endothelial cell apoptotic process / 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 / PECAM1 interactions / Fc-epsilon receptor signaling pathway / phosphatidylinositol-mediated signaling / Generation of second messenger molecules / RET signaling / positive regulation of blood vessel endothelial cell migration / Role of phospholipids in phagocytosis / glutamate receptor binding / 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 / FCGR3A-mediated IL10 synthesis / guanyl-nucleotide exchange factor activity / 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 / Schaffer collateral - CA1 synapse / Constitutive Signaling by EGFRvIII / modulation of chemical synaptic transmission / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / receptor tyrosine kinase binding / ISG15 antiviral mechanism / ruffle membrane / positive regulation of angiogenesis / cell-cell junction / Signaling by ALK fusions and activated point mutants / cell migration / lamellipodium / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / T cell receptor signaling pathway / host cell Golgi apparatus / in utero embryonic development / membrane => GO:0016020 / glutamatergic synapse / calcium ion binding / protein kinase binding / host cell plasma membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Herpesvirus Latent membrane 2 / Herpesvirus Latent membrane protein 2 / 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. ...Herpesvirus Latent membrane 2 / Herpesvirus Latent membrane protein 2 / 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 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 / 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
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 / Protein K15
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 8 strain GK18
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSsebyatika, G. / Krey, T.
CitationJournal: Plos Pathog. / Year: 2021
Title: Recruitment of phospholipase C gamma 1 to the non-structural membrane protein pK15 of Kaposi Sarcoma-associated herpesvirus promotes its Src-dependent phosphorylation.
Authors: Samarina, N. / Ssebyatika, G. / Tikla, T. / Waldmann, J.Y. / Abere, B. / Nanna, V. / Marasco, M. / Carlomagno, T. / Krey, T. / Schulz, T.F.
History
DepositionMar 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1
C: Protein K15
D: Protein K15


Theoretical massNumber of molelcules
Total (without water)29,7513
Polymers29,7513
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-14 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.66, 77.03, 59.96
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Isoform 2 of 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: 26569.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLCG1, PLC1 / Production host: Escherichia coli (E. coli)
References: UniProt: P19174, phosphoinositide phospholipase C
#2: Protein/peptide Protein K15


Mass: 1590.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 8 strain GK18 / References: UniProt: Q9QR69
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG 4000, 0.1M TrisHCl pH 8.5, 0.2M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→44.58 Å / Num. obs: 15318 / % possible obs: 99.5 % / Redundancy: 7.07 % / CC1/2: 0.998 / Rrim(I) all: 0.085 / Net I/σ(I): 12.19
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 7.25 % / Num. unique obs: 15318 / CC1/2: 0.895 / Rrim(I) all: 0.809 / % possible all: 97.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FBN

4fbn


Resolution: 2.1→44.58 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / SU R Cruickshank DPI: 0.263 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.266 / SU Rfree Blow DPI: 0.232 / SU Rfree Cruickshank DPI: 0.233
RfactorNum. reflection% reflectionSelection details
Rfree0.3138 766 -RANDOM
Rwork0.2496 ---
obs0.2526 15318 99.8 %-
Displacement parametersBiso mean: 62.95 Å2
Baniso -1Baniso -2Baniso -3
1--15.4243 Å20 Å20 Å2
2--7.1591 Å20 Å2
3---8.2653 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 0 0 32 1929
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081941HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.922614HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d680SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes328HARMONIC5
X-RAY DIFFRACTIONt_it1941HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion232SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1377SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.46
X-RAY DIFFRACTIONt_other_torsion15.72
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection% reflection
Rfree0.4806 20 -
Rwork0.3478 --
obs0.3538 404 99.24 %
Refinement TLS params.Origin x: -12.264 Å / Origin y: 8.4189 Å / Origin z: -14.0025 Å
111213212223313233
T-0.0926 Å2-0.065 Å20.0223 Å2--0.0376 Å2-0.0072 Å2---0.1951 Å2
L0.3608 °2-0.0158 °2-0.1055 °2-6.1024 °2-1.7866 °2--3.9761 °2
S0.0011 Å °0.0597 Å °-0.1526 Å °0.0597 Å °-0.1299 Å °0.3775 Å °-0.1526 Å °0.3775 Å °0.1288 Å °
Refinement TLS groupSelection details: { A|* }

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