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- PDB-1x9x: Solution Structure of Dimeric SAM Domain from MAPKKK Ste11 -

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Basic information

Entry
Database: PDB / ID: 1x9x
TitleSolution Structure of Dimeric SAM Domain from MAPKKK Ste11
ComponentsSerine/threonine-protein kinase STE11
KeywordsTRANSFERASE / SAM domain / MAP kinase / Ste11
Function / homology
Function and homology information


cell integrity MAPK cascade / osmosensory signaling pathway via Sho1 osmosensor / signal transduction involved in filamentous growth / pheromone response MAPK cascade / SAM domain binding / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / mitogen-activated protein kinase kinase kinase / Oxidative Stress Induced Senescence ...cell integrity MAPK cascade / osmosensory signaling pathway via Sho1 osmosensor / signal transduction involved in filamentous growth / pheromone response MAPK cascade / SAM domain binding / pseudohyphal growth / pheromone-dependent signal transduction involved in conjugation with cellular fusion / invasive growth in response to glucose limitation / mitogen-activated protein kinase kinase kinase / Oxidative Stress Induced Senescence / p38MAPK cascade / MAP kinase kinase kinase activity / protein kinase activity / phosphorylation / protein serine kinase activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 ...Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Ras-binding domain of Byr2 / Transcription Factor, Ets-1 / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Serine/threonine-protein kinase STE11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distant geometry
AuthorsBhattacharjya, S. / Xu, P. / Gingras, R. / Shaykhutdinov, R. / Wu, C. / Whiteway, M. / Ni, F.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution structure of the dimeric SAM domain of MAPKKK Ste11 and its interactions with the adaptor protein Ste50 from the budding yeast: implications for Ste11 activation and signal ...Title: Solution structure of the dimeric SAM domain of MAPKKK Ste11 and its interactions with the adaptor protein Ste50 from the budding yeast: implications for Ste11 activation and signal transmission through the Ste50-Ste11 complex.
Authors: Bhattacharjya, S. / Xu, P. / Gingras, R. / Shaykhutdinov, R. / Wu, C. / Whiteway, M. / Ni, F.
History
DepositionAug 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2005Provider: 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_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
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: Serine/threonine-protein kinase STE11
B: Serine/threonine-protein kinase STE11


Theoretical massNumber of molelcules
Total (without water)15,9202
Polymers15,9202
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)8 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Serine/threonine-protein kinase STE11


Mass: 7960.182 Da / Num. of mol.: 2 / Fragment: SAM domain (residues 37-104)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STE11 / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P23561, EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
222Filtered NOESY
NMR detailsText: Structure has been determined by 3-D NMR

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM Ste11 SAM, U-15N, 13C, 10mM phosphate buffer, 300 mM NaCl, 90% H2O, 10% D2O90% H2O/10% D2O
20.8mM Ste11 SAM U-15N, 13C mixed with unlabelled Ste11 SAM, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 300 mM NaCl / pH: 5.8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.6Guentertstructure solution
CYANA1.0.6Guentertrefinement
RefinementMethod: distant geometry / Software ordinal: 1
Details: Total distant constraints used, 1, 140, inter-subnuint NOE: 40, intra-subunit NOE:1134, dihedral angle:60
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 8

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