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- PDB-1v9v: Solution structure of putative domain of human KIAA0561 protein -

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Basic information

Entry
Database: PDB / ID: 1v9v
TitleSolution structure of putative domain of human KIAA0561 protein
ComponentsKIAA0561 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 4 helix bundle / MAST205 / microtubule-associated serine/threonine protein kinase / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cytoskeleton organization / non-specific serine/threonine protein kinase / intracellular signal transduction / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
MAST3 pre-PK domain-like / Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / hypothetical protein mp506/mpn330, domain 1 / PDZ domain 6 / PDZ domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. ...MAST3 pre-PK domain-like / Microtubule-associated serine/threonine-protein kinase, domain / Microtubule-associated serine/threonine-protein kinase, pre-PK domain superfamily / Microtubule-associated serine/threonine-protein kinase, catalytic domain / Domain of unknown function (DUF1908) / hypothetical protein mp506/mpn330, domain 1 / PDZ domain 6 / PDZ domain / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated serine/threonine-protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of putative domain of human KIAA0561 protein
Authors: Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionFeb 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: 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: KIAA0561 protein


Theoretical massNumber of molelcules
Total (without water)12,4261
Polymers12,4261
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 KIAA0561 protein


Mass: 12426.110 Da / Num. of mol.: 1 / Fragment: putative domain (residues 180-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: KAZUSA cDNA hh01676 / Plasmid: P030723-16 / References: UniProt: O60307

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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 putative domain U-15N, 13C; 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: 7.0 / 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
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.853Kobayashi, 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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