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- PDB-2pph: solution structure of human MEKK3 PB1 domain -

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Basic information

Entry
Database: PDB / ID: 2pph
Titlesolution structure of human MEKK3 PB1 domain
ComponentsMitogen-activated protein kinase kinase kinase 3
KeywordsTRANSFERASE / kinase signaling domain
Function / homology
Function and homology information


positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction ...positive regulation of cell proliferation in bone marrow / mitogen-activated protein kinase kinase kinase / positive regulation of p38MAPK cascade / positive regulation of cell migration involved in sprouting angiogenesis / blood vessel development / negative regulation of cellular senescence / MAP kinase kinase kinase activity / Interleukin-1 signaling / MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / protein autophosphorylation / protein kinase activity / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll ...Mitogen-activated protein kinase kinase kinase 2/3, PB1 domain / PB1 domain / PB1 domain / PB1 domain profile. / PB1 domain / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Alpha Beta
Similarity search - Domain/homology
Mitogen-activated protein kinase kinase kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsHu, Q. / Zhang, J. / Wu, J. / Shi, Y.
CitationJournal: Biochemistry / Year: 2007
Title: Insight into the Binding Properties of MEKK3 PB1 to MEK5 PB1 from Its Solution Structure.
Authors: Hu, Q. / Shen, W. / Huang, H. / Liu, J. / Zhang, J. / Huang, X. / Wu, J. / Shi, Y.
History
DepositionApr 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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
Revision 1.4May 22, 2024Group: 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: Mitogen-activated protein kinase kinase kinase 3


Theoretical massNumber of molelcules
Total (without water)11,1871
Polymers11,1871
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Mitogen-activated protein kinase kinase kinase 3 / MAPK/ERK kinase kinase 3 / MEK kinase 3 / MEKK 3


Mass: 11186.697 Da / Num. of mol.: 1 / Fragment: PB1 domain (Residues 42-126)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MEKK3 / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q99759, mitogen-activated protein kinase kinase 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
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

DetailsContents: 0.5mM 15N,13C-labeled MEKK3 PB1 50mM phosphate buffer (pH 6.0), 1mM EDTA,10%(v/v) D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2F.Delaglioprocessing
CNS1.1A.T.Brungerstructure solution
CSI1David S. Wishartdata analysis
MOLMOL2k.2Koradidata analysis
CNS1.1A.T.Brungerrefinement
RefinementMethod: Distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 1335 restraints, 1197 are NOE-derived distance constraints, 110 dihedral angle restraints,28 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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