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- PDB-2rqw: Solution structure of Bem1p SH3CI domain complexed with Ste20p-PR... -

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Basic information

Entry
Database: PDB / ID: 2rqw
TitleSolution structure of Bem1p SH3CI domain complexed with Ste20p-PRR peptide
Components
  • 24-meric peptide from Serine/threonine-protein kinase STE20
  • Bud emergence protein 1
KeywordsSIGNALING PROTEIN / Bem1p / Ste20p / SH3CI / PRR / Cytoplasm / Cytoskeleton / SH3 domain / Cell cycle / Pheromone response / Serine/threonine-protein kinase
Function / homology
Function and homology information


sterol import / negative regulation of sterol import / CD28 dependent Vav1 pathway / osmosensory signaling pathway via Sho1 osmosensor / positive regulation of vacuole fusion, non-autophagic / RHO GTPases activate PAKs / signal transduction involved in filamentous growth / bipolar cellular bud site selection / RHO GTPases Activate NADPH Oxidases / RHOD GTPase cycle ...sterol import / negative regulation of sterol import / CD28 dependent Vav1 pathway / osmosensory signaling pathway via Sho1 osmosensor / positive regulation of vacuole fusion, non-autophagic / RHO GTPases activate PAKs / signal transduction involved in filamentous growth / bipolar cellular bud site selection / RHO GTPases Activate NADPH Oxidases / RHOD GTPase cycle / RHOV GTPase cycle / budding cell apical bud growth / conjugation with cellular fusion / RHOQ GTPase cycle / cell morphogenesis involved in conjugation with cellular fusion / response to pheromone triggering conjugation with cellular fusion / site of polarized growth / Regulation of actin dynamics for phagocytic cup formation / RHOU GTPase cycle / pseudohyphal growth / PAR polarity complex / pheromone-dependent signal transduction involved in conjugation with cellular fusion / cellular bud site selection / invasive growth in response to glucose limitation / vacuole inheritance / MAP kinase kinase kinase kinase activity / incipient cellular bud site / cellular bud tip / maintenance of protein location / regulation of exit from mitosis / cellular bud neck / regulation of Rho protein signal transduction / mating projection tip / phosphatidylinositol-3-phosphate binding / MAPK6/MAPK4 signaling / regulation of MAPK cascade / stress granule assembly / cellular response to starvation / cellular response to hydrogen peroxide / MAPK cascade / cell cortex / protein-macromolecule adaptor activity / molecular adaptor activity / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of apoptotic process / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / mRNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / p21 activated kinase binding domain / : / PB1 domain / PB1 domain / CRIB domain superfamily / P21-Rho-binding domain ...Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / : / p21 activated kinase binding domain / : / PB1 domain / PB1 domain / CRIB domain superfamily / P21-Rho-binding domain / : / PB1 domain profile. / CRIB domain profile. / P21-Rho-binding domain / CRIB domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / SH3 Domains / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
Bud emergence protein 1 / Serine/threonine-protein kinase STE20
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsTakaku, T. / Ogura, K. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Solution structure of a novel Cdc42-binding module of Bem1 and its interaction with Ste20 and Cdc42
Authors: Takaku, T. / Ogura, K. / Kumeta, H. / Yoshida, N. / Inagaki, F.
History
DepositionDec 21, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bud emergence protein 1
B: 24-meric peptide from Serine/threonine-protein kinase STE20


Theoretical massNumber of molelcules
Total (without water)13,7472
Polymers13,7472
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1386.5 Å2
ΔGint-10.4 kcal/mol
Surface area9136.3 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Bud emergence protein 1 / Bem1p / Suppressor of RHO3 protein 1


Mass: 11414.939 Da / Num. of mol.: 1 / Fragment: SH3CI domain, residues 156-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P29366
#2: Protein/peptide 24-meric peptide from Serine/threonine-protein kinase STE20 / Ste20p-PRR peptide


Mass: 2331.562 Da / Num. of mol.: 1 / Fragment: BEM1-binding domain, residues 463-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q03497

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.5mM [U-99% 13C; U-99% 15N] protein; 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.5 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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