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- PDB-2kfj: Solution structure of the loop deletion mutant of PB1 domain of Cdc24p -

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Basic information

Entry
Database: PDB / ID: 2kfj
TitleSolution structure of the loop deletion mutant of PB1 domain of Cdc24p
ComponentsCell division control protein 24
KeywordsSIGNALING PROTEIN / PB1 / Cdc24p / yeast / Guanine-nucleotide releasing factor / Phosphoprotein
Function / homology
Function and homology information


regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / septin ring organization / protein localization to cell cortex / division septum / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip ...regulation of pheromone-dependent signal transduction involved in conjugation with cellular fusion / chemotropism / Cdc24p-Far1p-Gbetagamma complex / septin ring organization / protein localization to cell cortex / division septum / PAR polarity complex / cellular bud site selection / incipient cellular bud site / cellular bud tip / regulation of exit from mitosis / cellular bud neck / mating projection tip / regulation of Rho protein signal transduction / establishment of cell polarity / guanyl-nucleotide exchange factor activity / cell cortex / intracellular signal transduction / nucleus / cytoplasm
Similarity search - Function
Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PB1 domain profile. / PB1 domain / Calponin homology domain ...Cdc24/Scd1, N-terminal / Rho guanine nucleotide exchange factor Cdc24/Scd1, PH domain / CDC24 Calponin / Pleckstrin homology domain / PB1 domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / PB1 domain profile. / PB1 domain / 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 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsOgura, K. / Tandai, T. / Yoshinaga, S. / Kobashigawa, Y. / Kumeta, H. / 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 22, 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: Cell division control protein 24


Theoretical massNumber of molelcules
Total (without water)10,0501
Polymers10,0501
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell division control protein 24 / Calcium regulatory protein


Mass: 10050.368 Da / Num. of mol.: 1 / Fragment: PB1 domain
Mutation: Asn770-Ser777 and Asn807-Asn809 are deleted by mutation.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC24, CLS4, YAL041W / 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
1213D 1H-13C NOESY
1312D 1H-15N HSQC
1413D HNCO
1513D HN(CA)CB

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Sample preparation

DetailsContents: 1.0mM [U-99% 13C; U-99% 15N] PB1-domain, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1.0 mM / Component: entity-1 / Isotopic labeling: [U-99% 13C; U-99% 15N]
Sample conditionsIonic strength: 150 sodium chloride / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / 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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