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- PDB-1xx0: Structure of the C-terminal PH domain of human pleckstrin -

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Basic information

Entry
Database: PDB / ID: 1xx0
TitleStructure of the C-terminal PH domain of human pleckstrin
ComponentsPleckstrin
KeywordsLIPID BINDING PROTEIN / pleckstrin / PH / C-terminal / pleckstrin homology
Function / homology
Function and homology information


positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / negative regulation of calcium-mediated signaling / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation ...positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / negative regulation of calcium-mediated signaling / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation / negative regulation of G protein-coupled receptor signaling pathway / phosphatidylinositol metabolic process / positive regulation of actin filament bundle assembly / positive regulation of integrin activation / cell projection organization / vesicle docking involved in exocytosis / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of platelet activation / cortical actin cytoskeleton organization / hematopoietic progenitor cell differentiation / integrin-mediated signaling pathway / protein kinase C binding / platelet aggregation / ruffle membrane / Platelet degranulation / actin cytoskeleton organization / protein homodimerization activity / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Pleckstrin, DEP domain / : / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...Pleckstrin, DEP domain / : / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsEdlich, C. / Stier, G. / Simon, B. / Sattler, M. / Muhle-Goll, C.
CitationJournal: STRUCTURE / Year: 2005
Title: Structure and phosphatidylinositol-(3,4)-bisphosphate binding of the C-terminal PH domain of human pleckstrin
Authors: Edlich, C. / Stier, G. / Simon, B. / Sattler, M. / Muhle-Goll, C.
History
DepositionNov 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pleckstrin


Theoretical massNumber of molelcules
Total (without water)14,7961
Polymers14,7961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 80structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Pleckstrin / / Platelet p47 protein


Mass: 14795.972 Da / Num. of mol.: 1 / Fragment: C-terminal PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEK / Plasmid: pET9d_mod / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: This structure was determined using standard heteronuclear techniques.

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Sample preparation

DetailsContents: 0.5mM C-PH, U-15N,13C; 20mM sodium phosphate buffer pH 6.8, 100mM NaCl, 0.02% NaN3
Solvent system: 10% D2O, 90% H2O, 100% D2O
Sample conditionsIonic strength: 100mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 295 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX8002
Bruker DRXBrukerDRX9003

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, J.P., O'Donoghue S.I., Nilges M.structure solution
ARIA1.2Linge, J.P., O'Donoghue S.I., Nilges M.refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 80 / Conformers submitted total number: 10

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