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- PDB-1ul7: Solution structure of kinase associated domain 1 of mouse MAP/mic... -

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Basic information

Entry
Database: PDB / ID: 1ul7
TitleSolution structure of kinase associated domain 1 of mouse MAP/microtubule affinity-regulating kinase 3
ComponentsMAP/microtubule affinity-regulating kinase 3
KeywordsTRANSFERASE / KA1 domain / ELKL motif / MARK3 / STRUCTURAL GENOMICS / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Negative regulation of MAPK pathway / RAF activation / Transcriptional and post-translational regulation of MITF-M expression and activity / MAP2K and MAPK activation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / regulation of G2/M transition of mitotic cell cycle / non-specific serine/threonine protein kinase / protein phosphorylation ...Negative regulation of MAPK pathway / RAF activation / Transcriptional and post-translational regulation of MITF-M expression and activity / MAP2K and MAPK activation / negative regulation of protein localization to nucleus / tau-protein kinase activity / negative regulation of hippo signaling / regulation of G2/M transition of mitotic cell cycle / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / Kinase associated domain 1, KA1 / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / TATA-Binding Protein / Ubiquitin associated domain / Ubiquitin-associated domain ...: / Kinase associated domain 1, KA1 / Kinase associated domain 1 (KA1) / Kinase associated domain 1 / Kinase associated domain 1 (KA1) profile. / KA1 domain/Ssp2, C-terminal / UBA/TS-N domain / TATA-Binding Protein / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MAP/microtubule affinity-regulating kinase 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsTochio, N. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2006
Title: Solution structure of the kinase-associated domain 1 of mouse microtubule-associated protein/microtubule affinity-regulating kinase 3
Authors: Tochio, N. / Koshiba, S. / Kobayashi, N. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Motoda, Y. / Kobayashi, A. / Tanaka, A. / Hayashizaki, Y. / Terada, T. / ...Authors: Tochio, N. / Koshiba, S. / Kobayashi, N. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Tomo, Y. / Motoda, Y. / Kobayashi, A. / Tanaka, A. / Hayashizaki, Y. / Terada, T. / Shirouzu, M. / Kigawa, T. / Yokoyama, S.
History
DepositionSep 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2004Provider: 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
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP/microtubule affinity-regulating kinase 3


Theoretical massNumber of molelcules
Total (without water)11,5331
Polymers11,5331
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 least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

#1: Protein MAP/microtubule affinity-regulating kinase 3 / MPK-10 / ELKL motif kinase 2


Mass: 11533.256 Da / Num. of mol.: 1 / Fragment: kinase associated domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA 1600015G02, Mark3, Emk2, Mpk10 / Plasmid: P021202-01
References: UniProt: Q03141, non-specific serine/threonine protein kinase

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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: 1.0mM KA1 domain U-15N, 13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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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
KUJIRA0.853Kobayashi, 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, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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