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- PDB-1wj1: Solution structure of phosphotyrosine interaction domain of mouse... -

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Basic information

Entry
Database: PDB / ID: 1wj1
TitleSolution structure of phosphotyrosine interaction domain of mouse Numb protein
ComponentsNumb protein
KeywordsSIGNALING PROTEIN / PTB / PID domain / Numb protein / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


neuroblast division in subventricular zone / regulation of postsynapse assembly / Degradation of GLI1 by the proteasome / lateral ventricle development / Hedgehog 'on' state / Recycling pathway of L1 / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization ...neuroblast division in subventricular zone / regulation of postsynapse assembly / Degradation of GLI1 by the proteasome / lateral ventricle development / Hedgehog 'on' state / Recycling pathway of L1 / alpha-catenin binding / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of protein localization to plasma membrane / adherens junction organization / positive regulation of dendrite morphogenesis / clathrin-coated vesicle / positive regulation of neurogenesis / regulation of neuron differentiation / neuroblast proliferation / clathrin-coated pit / forebrain development / axonogenesis / beta-catenin binding / apical part of cell / nervous system development / cytoplasmic vesicle / basolateral plasma membrane / dendritic spine / postsynaptic density / early endosome / endosome membrane / positive regulation of cell migration / cadherin binding / glutamatergic synapse / plasma membrane / cytoplasm
Similarity search - Function
NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Protein numb homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSato, M. / Tomizawa, T. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of phosphotyrosine interaction domain of mouse Numb protein
Authors: Sato, M. / Tomizawa, T. / Koshiba, S. / Tochio, N. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 28, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 28, 2004Provider: 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 700SHEET AUTHOR DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Numb protein


Theoretical massNumber of molelcules
Total (without water)17,2271
Polymers17,2271
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)20 / 100structures with the least restraint violations, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Numb protein


Mass: 17226.615 Da / Num. of mol.: 1 / Fragment: PID domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1200002O22 / Plasmid: P031020-52 / References: UniProt: Q9QZS3

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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: 1.3mM PID domain U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6.0 / 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
KUJIRA0.8996Kobayashi, 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: structures with the least restraint violations, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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