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- PDB-1w4m: Structure of the human pleckstrin DEP domain by multidimensional NMR -

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Basic information

Entry
Database: PDB / ID: 1w4m
TitleStructure of the human pleckstrin DEP domain by multidimensional NMR
ComponentsPLECKSTRIN
KeywordsSIGNAL TRANSDUCTION / DEP DOMAIN / HUMAN PLECKSTRIN
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 / simulated annealing
AuthorsCivera, C. / Simon, B. / Stier, G. / Sattler, M. / Macias, M.J.
CitationJournal: Proteins: Struct.,Funct., Genet. / Year: 2005
Title: Structure and Dynamics of the Human Pleckstrin Dep Domain: Distinct Molecular Features of a Novel Dep Domain Subfamily
Authors: Civera, C. / Simon, B. / Stier, G. / Sattler, M. / Macias, M.J.
History
DepositionJul 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: PLECKSTRIN


Theoretical massNumber of molelcules
Total (without water)11,4631
Polymers11,4631
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)10 / 100LOWEST ENERGY
RepresentativeModel #1

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Components

#1: Protein PLECKSTRIN / HUMAN PLECKSTRIN DEP DOMAIN / PLATELET P47 PROTEIN


Mass: 11462.791 Da / Num. of mol.: 1 / Fragment: HUMAN DEP DOMAIN, RESIDUES 121-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET9D, PETM30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08567

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D HOMONUCLEAR TOCSY AND NOESY
1211H-15N-HSQC
131HNCA
141CBCANH
151CBCA(CO)NH
161HNCO
171(H)CC(CO)NH
181C(CO)NH
191(H)CCH-TOCSY
1101HBHA(CO)NH
1111HBCBCCDHD
1121HBCBCCDCEHE3D
113113C-EDITED TOCSY
11411H-15N-HNHA
1151IPAP 1H-15N-HSQC
NMR detailsText: NONE

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Sample preparation

DetailsContents: 20MM PHOSPHATE BUFFER, 30MM NACL, 3MM DITHIOTHREITOL (DTT), 0. 03% (W/V) NAN3 IN 90% H2O / 10% D2O OR 100% D2O
Sample conditionsIonic strength: 30 mM / pH: 6.5 / Temperature: 295.0 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
ARIA CNSCNSstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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