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- PDB-2kfk: Solution structure of Bem1p PB1 domain complexed with Cdc24p PB1 ... -

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Basic information

Entry
Database: PDB / ID: 2kfk
TitleSolution structure of Bem1p PB1 domain complexed with Cdc24p PB1 domain
Components
  • Bud emergence protein 1
  • Cell division control protein 24
KeywordsSIGNALING PROTEIN / PB1 / budding / yeast / Phox
Function / homology
Function and homology information


regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / RHO GTPases Activate NADPH Oxidases / septin ring organization / protein localization to cell cortex / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / division septum / PAR polarity complex ...regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / RHO GTPases Activate NADPH Oxidases / septin ring organization / protein localization to cell cortex / conjugation with cellular fusion / cell morphogenesis involved in conjugation with cellular fusion / division septum / PAR polarity complex / site of polarized growth / superoxide-generating NADPH oxidase activator activity / cellular bud site selection / incipient cellular bud site / cellular bud tip / maintenance of protein location / regulation of exit from mitosis / cellular bud neck / mating projection tip / regulation of Rho protein signal transduction / phosphatidylinositol-3-phosphate binding / superoxide anion generation / establishment of cell polarity / guanyl-nucleotide exchange factor activity / protein-macromolecule adaptor activity / cell cortex / molecular adaptor activity / cytoskeleton / intracellular signal transduction / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. ...Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / Bem1/Scd2, SH3 domain 1 / Bem1/Scd2, SH3 domain 2 / Bem1/Scd2, PX domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PB1 domain profile. / PB1 domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Calponin homology domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Src homology 3 domains / Ubiquitin-like (UB roll) / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 24 / Bud emergence protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKobashigawa, Y. / Yoshinaga, S. / Tandai, T. / Ogura, K. / Inagaki, F.
CitationJournal: J.Biochem. / Year: 2009
Title: NMR structure of the heterodimer of Bem1 and Cdc24 PB1 domains from Saccharomyces cerevisiae
Authors: Ogura, K. / Tandai, T. / Yoshinaga, S. / Kobashigawa, Y. / Kumeta, H. / Ito, T. / Sumimoto, H. / Inagaki, F.
History
DepositionFeb 23, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 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: Bud emergence protein 1
B: Cell division control protein 24


Theoretical massNumber of molelcules
Total (without water)19,0312
Polymers19,0312
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 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 9037.458 Da / Num. of mol.: 1 / Fragment: UNP residues 477-551
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 Cell division control protein 24 / Calcium regulatory protein


Mass: 9993.317 Da / Num. of mol.: 1 / Fragment: UNP residues 761-854 / Mutation: DELETE UNP RESIDUES 770-777, 807-809
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P11433

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-15N NOESY
1223D 1H-15N NOESY
1313D 1H-13C NOESY
1423D 1H-13C NOESY
1533D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM [U-98% 13C; U-98% 15N] Bem1p-1, 1mM Cdc24p-2, 90% H2O/10% D2O90% H2O/10% D2O
21mM Bem1p-3, 1mM [U-98% 13C; U-98% 15N] Cdc24p-4, 90% H2O/10% D2O90% H2O/10% D2O
31mM Bem1p-5, 1mM [U-2H] Cdc24p-6, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMBem1p-1[U-98% 13C; U-98% 15N]1
1 mMCdc24p-21
1 mMBem1p-32
1 mMCdc24p-4[U-98% 13C; U-98% 15N]2
1 mMBem1p-53
1 mMCdc24p-6[U-2H]3
Sample conditionsIonic strength: 0.15 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1

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