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- PDB-1wi0: Solution structure of the PB1 domain of mouse mitogen activated p... -

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Basic information

Entry
Database: PDB / ID: 1wi0
TitleSolution structure of the PB1 domain of mouse mitogen activated protein kinase kinase 5 (MAP2K5)
ComponentsMitogen activated protein kinase kinase 5
KeywordsTRANSFERASE / PB1 domain / protein-protein interaction site / cytoplasmic signalling / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / : / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / MAP kinase kinase activity ...ERK5 cascade / negative regulation of chemokine (C-X-C motif) ligand 2 production / : / negative regulation of response to cytokine stimulus / negative regulation of heterotypic cell-cell adhesion / negative regulation of interleukin-8 production / mitogen-activated protein kinase kinase / negative regulation of cell migration involved in sprouting angiogenesis / negative regulation of NF-kappaB transcription factor activity / MAP kinase kinase activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of protein metabolic process / positive regulation of epithelial cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle / cellular response to growth factor stimulus / MAPK cascade / heart development / positive regulation of cell growth / protein tyrosine kinase activity / protein kinase activity / protein phosphorylation / protein serine/threonine kinase activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Dual specificity mitogen-activated protein kinase kinase 5, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Dual specificity mitogen-activated protein kinase kinase 5, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
Dual specificity mitogen-activated protein kinase kinase 5
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYoneyama, M. / Hayashi, F. / 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 PB1 domain of mouse mitogen activated protein kinase kinase 5 (MAP2K5)
Authors: Yoneyama, M. / Hayashi, F. / Tochio, N. / Koshiba, S. / 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_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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen activated protein kinase kinase 5


Theoretical massNumber of molelcules
Total (without water)12,4091
Polymers12,4091
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 Mitogen activated protein kinase kinase 5 / MAP2K5


Mass: 12408.806 Da / Num. of mol.: 1 / Fragment: PB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis / Gene: RIKEN cDNA A230106F01 / Plasmid: P031125-28
References: UniProt: Q9WVS7, 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 15N-separated NOESY
1223D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM PB1 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: 297 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
NMRView5.0.4Jhonson, B.A.data analysis
KUJIRA0.896Kobayashi, N.data analysis
CYANA1.0.8Guentert, P.structure solution
NMRPipe20020425Delaglio, F.processing
CYANA1.0.8Guentert, 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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