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- PDB-1v5m: Solution Structure of the Pleckstrin Homology Domain of Mouse APS -

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Entry
Database: PDB / ID: 1v5m
TitleSolution Structure of the Pleckstrin Homology Domain of Mouse APS
ComponentsSH2 and PH domain-containing adapter protein APS
KeywordsPROTEIN BINDING / adaptor protein / Pleckstrin Homology domain / cellular signaling / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


antigen receptor-mediated signaling pathway / Regulation of KIT signaling / regulation of Ras protein signal transduction / Factors involved in megakaryocyte development and platelet production / B-1 B cell homeostasis / regulation of metabolic process / negative regulation of glucose import / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of immune response / signaling adaptor activity ...antigen receptor-mediated signaling pathway / Regulation of KIT signaling / regulation of Ras protein signal transduction / Factors involved in megakaryocyte development and platelet production / B-1 B cell homeostasis / regulation of metabolic process / negative regulation of glucose import / transmembrane receptor protein tyrosine kinase adaptor activity / regulation of immune response / signaling adaptor activity / brown fat cell differentiation / stress fiber / ruffle / SH2 domain binding / actin filament / B cell receptor signaling pathway / cytokine-mediated signaling pathway / insulin receptor signaling pathway / glucose homeostasis / nervous system development / actin cytoskeleton organization / intracellular signal transduction / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
SH2B adapter protein 2 / SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. ...SH2B adapter protein 2 / SH2B2, SH2 domain / Phenylalanine zipper / Phenylalanine zipper superfamily / Phenylalanine zipper / SH2B adapter protein / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
SH2B adapter protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLi, H. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of the Pleckstrin Homology Domain of Mouse APS
Authors: Li, H. / Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionNov 25, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: 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 1.4Dec 27, 2023Group: 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: SH2 and PH domain-containing adapter protein APS


Theoretical massNumber of molelcules
Total (without water)14,6901
Polymers14,6901
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SH2 and PH domain-containing adapter protein APS


Mass: 14689.724 Da / Num. of mol.: 1 / Fragment: Pleckstrin Homology Domain / Mutation: T8N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 5730427K19 / Plasmid: P030212-26 / References: UniProt: Q9JID9

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Experimental details

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Experiment

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

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Sample preparation

DetailsContents: 1.23mM Pleckstrin Homology domain U-13C, 15N; 20mM d-Tris-HCl(7.5); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.854Kobayashi, N.data analysis
CYANA2.0.17Guentert, P.structure solution
CYANA2.0.17Guentert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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