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- PDB-2byf: NMR solution structure of phospholipase c epsilon RA 2 domain -

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Basic information

Entry
Database: PDB / ID: 2byf
TitleNMR solution structure of phospholipase c epsilon RA 2 domain
ComponentsPHOSPHOLIPASE C, EPSILON 1
KeywordsLIPASE / PHOSPHOLIPASE C EPSILON / RAS BINDING DOMAIN / UBIQUITIN SUPERFOLD
Function / homology
Function and homology information


phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol phospholipase C activity / glomerulus development / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol-mediated signaling / positive regulation of lamellipodium assembly / lipid catabolic process ...phosphoinositide phospholipase C / diacylglycerol biosynthetic process / phosphatidylinositol metabolic process / phospholipase C activity / phosphatidylinositol phospholipase C activity / glomerulus development / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol-mediated signaling / positive regulation of lamellipodium assembly / lipid catabolic process / release of sequestered calcium ion into cytosol / guanyl-nucleotide exchange factor activity / calcium-mediated signaling / epidermal growth factor receptor signaling pathway / small GTPase binding / lamellipodium / phospholipase C-activating G protein-coupled receptor signaling pathway / Ras protein signal transduction / intracellular signal transduction / G protein-coupled receptor signaling pathway / Golgi membrane / enzyme binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / 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 ...1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / : / : / Phosphoinositide-specific phospholipase C, EF-hand-like domain / Phosphoinositide-specific phospholipase C, efhand-like / 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 / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / 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. / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / C2 domain superfamily / Ubiquitin-like (UB roll) / EF-hand domain pair / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1 / 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / RESTRAINED SIMULATED ANNEALING, WATER REFINEMENT
AuthorsBunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Gieschik, P. / Pearl, L.H. ...Bunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Gieschik, P. / Pearl, L.H. / Driscoll, P.C. / Katan, M.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural and Mechanistic Insights Into Ras Association Domains of Phospholipase C Epsilon.
Authors: Bunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Sorli, S.C. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Ponting, C.P. / Gierschik, P. / Pearl, L.H. / ...Authors: Bunney, T.D. / Harris, R. / Gandarillas, N.L. / Josephs, M.B. / Roe, S.M. / Sorli, S.C. / Paterson, H.F. / Rodrigues-Lima, F. / Esposito, D. / Ponting, C.P. / Gierschik, P. / Pearl, L.H. / Driscoll, P.C. / Katan, M.
History
DepositionAug 1, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOLIPASE C, EPSILON 1


Theoretical massNumber of molelcules
Total (without water)13,1071
Polymers13,1071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ENERGY STRUCTURE WITH NO RESTRAINT VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein PHOSPHOLIPASE C, EPSILON 1 / PHOSPHOLIPASE C EPSILON


Mass: 13106.789 Da / Num. of mol.: 1 / Fragment: RA2 DOMAIN, RESIDUES 2131-2246 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRIEX4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q5VWL5, UniProt: Q9P212*PLUS
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 2150 TO LEU

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111C13-NOESY
221N15-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN.

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Sample preparation

DetailsContents: 90% WATER, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1275 mM6.51.0 atm298.0 K
22756.51.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
Xplor-NIHC.D. SCHWIETERS, J.J. KUSZEWSKI, N. TJrefinement
ANSIGstructure solution
CNSstructure solution
Xplor-NIHstructure solution
RefinementMethod: RESTRAINED SIMULATED ANNEALING, WATER REFINEMENT / Software ordinal: 1
Details: AB INITIO SIMULATED ANNEALING PROTOCOL WITH CARTESIAN MOLECULAR DYNAMICS AND TORSION ANGLE DYNAMICS SIMULATED ANNEALING. A FINAL STEP OF RESTRAINED MOLECULAR DYNAMICS WITH EXPLICIT INCLUSION OF SOLVENT.
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURE WITH NO RESTRAINT VIOLATIONS
Conformers calculated total number: 100 / Conformers submitted total number: 20

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