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- PDB-2cso: Solution structure of the DEP domain of human pleckstrin -

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Basic information

Entry
Database: PDB / ID: 2cso
TitleSolution structure of the DEP domain of human pleckstrin
ComponentsPleckstrin
KeywordsSIGNALING PROTEIN / DEP domain / Pleckstrin / Platelet p47 protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / protein secretion by platelet / regulation of cell diameter / negative regulation of inositol phosphate biosynthetic process / positive regulation of actin filament depolymerization / platelet degranulation / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of actin filament bundle assembly / phosphatidylinositol metabolic process / positive regulation of integrin activation ...: / protein secretion by platelet / regulation of cell diameter / negative regulation of inositol phosphate biosynthetic process / positive regulation of actin filament depolymerization / platelet degranulation / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / positive regulation of actin filament bundle assembly / phosphatidylinositol metabolic process / positive regulation of integrin activation / 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 / thrombin-activated receptor signaling pathway / hematopoietic progenitor cell differentiation / protein kinase C binding / integrin-mediated signaling pathway / platelet aggregation / ruffle membrane / Platelet degranulation / actin cytoskeleton organization / phospholipase C-activating G protein-coupled receptor signaling pathway / intracellular signal transduction / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / PH-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsInoue, K. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Solution structure of the DEP domain of human pleckstrin
Authors: Inoue, K. / Hayashi, F. / Yokoyama, S.
History
DepositionMay 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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 / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)13,8521
Polymers13,8521
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 lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Pleckstrin / Platelet p47 protein


Mass: 13852.312 Da / Num. of mol.: 1 / Fragment: DEP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: PLEK, P47 / Plasmid: P040621-07 / 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
NMR detailsText: spectrometer_id 1 for 3D_15N_separated_NOESY, spectrometer_id 2 for 3D_13C_separated_NOESY

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Sample preparation

DetailsContents: 1.35mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9296Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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