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- PDB-1x05: Solution structure of the C-terminal PH domain of human pleckstrin -

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Basic information

Entry
Database: PDB / ID: 1x05
TitleSolution structure of the C-terminal PH domain of human pleckstrin
ComponentsPleckstrin
KeywordsSIGNALING PROTEIN / pleckstrin / PH domain / structural genomics / NPPSFA / RIKEN Structural Genomics/Proteomics Initiative / RSGI / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / phosphatidylinositol metabolic process ...positive regulation of inositol-polyphosphate 5-phosphatase activity / protein secretion by platelet / regulation of cell diameter / thrombin-activated receptor signaling pathway / negative regulation of inositol phosphate biosynthetic process / positive regulation of actin filament depolymerization / protein kinase C signaling / platelet degranulation / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / phosphatidylinositol metabolic process / positive regulation of integrin activation / positive regulation of actin filament bundle assembly / cell projection organization / ruffle organization / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of calcium-mediated signaling / positive regulation of platelet activation / vesicle docking involved in exocytosis / cortical actin cytoskeleton organization / negative regulation of G protein-coupled receptor signaling pathway / 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 / Roll / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the C-terminal PH domain of human pleckstrin
Authors: Li, H. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 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: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX Determination method: Author determined
Remark 700SHEET Determination method: Author determined

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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)14,3551
Polymers14,3551
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Pleckstrin / Platelet p47 protein


Mass: 14355.236 Da / Num. of mol.: 1 / Fragment: PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P040517-04 / References: UniProt: P08567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1.13mM PH domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 mM / pH: 7 / Pressure: ambient / Temperature: 296 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.913Kobayashi, N.data analysis
CYANA1.0.7Guentert, P.structure solution
CYANA1.0.7Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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