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- PDB-1uf0: Solution structure of the N-terminal DCX domain of human doubleco... -

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Basic information

Entry
Database: PDB / ID: 1uf0
TitleSolution structure of the N-terminal DCX domain of human doublecortin-like kinase
ComponentsSerine/threonine-protein kinase DCAMKL1
KeywordsTRANSFERASE / structural genomics / ubiquitin-like fold / microtubule-binding / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration ...central nervous system projection neuron axonogenesis / axon extension / negative regulation of protein localization to nucleus / dendrite morphogenesis / endosomal transport / protein localization to nucleus / forebrain development / neuron projection morphogenesis / central nervous system development / neuron migration / response to virus / nervous system development / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Doublecortin domain / Doublecortin / Doublecortin domain profile. / Domain in the Doublecortin (DCX) gene product / Doublecortin domain / Doublecortin domain superfamily / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase DCLK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsSaito, K. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the N-terminal DCX domain of human doublecortin-like kinase
Authors: Saito, K. / Kigawa, T. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionMay 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 1.4Dec 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: Serine/threonine-protein kinase DCAMKL1


Theoretical massNumber of molelcules
Total (without water)12,8341
Polymers12,8341
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase DCAMKL1 / doublecortin-like kinase KIAA0369


Mass: 12834.478 Da / Num. of mol.: 1 / Fragment: DCX domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: Kazusa cDNA hh00177 / Plasmid: P020924-51
References: UniProt: O15075, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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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: 1mM DCX domain U-15N,13C, 20mM phosphate buffer Na, 100mM NaCl, 1mM d-DTT, 0.2% NaN3, 90% H2O, 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
NMRView5Johnson, B.A.data analysis
CNS1.1structure solution
CNS1.1refinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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